💡 Need to consolidate a few Jira instances? Do it without data loss! [Use Case]

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How GitProtect backup & Disaster Recovery software and codefortynine’s Deep Clone for Jira simplify instance consolidation and secure your data

As organizations grow, so does the complexity of their Jira environments. New teams, new regions, or acquisitions can lead to each team having its own Jira setup. But over time, the disadvantages pile up: limited visibility between teams, duplication of administrative effort and data silos that slow everything down.

Consolidation in a single Jira instance sounds like the obvious solution. And it is, but only if it's done right.

If you underestimate the complexity of migration, you risk losing data and a lot of manual effort. With the right set of solutions, the challenges of a complex migration can be significantly reduced. Thus, you can optimize the process, secure what’s essential, and help teams move faster without losing context.

Why do you need to be cautious when consolidating Jira?

Well, in consolidating Jira instances, there lies a clear business value -  improve collaboration, centralize reporting, and simplify governance. However, such juggling with your data can also come with serious risks if it’s done without proper tooling. So, what can go wrong?

• You may lose your data or overwrite it, especially during bulk updates or project merges.
• If your linked work items, attachments, or custom fields aren’t properly mapped, they can be broken.
• There might arise a problem with user permissions and groups, as they probably won’t align between consolidated Jira instances.
• Manual cloning or exports can take a lot of time, especially if your Jira environment is big. Moreover, it doesn’t guarantee the data restore of your Jira data if something goes wrong.
• And the worst-case scenario? Data loss. Yeah, if something fails mid-way during the migration, without backup, there would be no way to roll back.

Smart app solutions can completely change this picture. Let’s look at an example of a Use Case - how with GitProtect backup & DR software for Jira Cloud and codefortynine’s Deep Clone for Jira, Jira Admins can streamline the entire consolidation process and have peace of mind that there is no risk of data loss. 

Consolidation starts: 3… 2…1… Go!

Let’s imagine a situation where a company that has grown through multiple acquisitions ends up with 3 separate Jira Cloud instances. Each team brought its own workflows, custom fields, and project configurations. Over time, this multi-instance setup became a real bottleneck. Why? No unified reporting, duplicated issue tracking, and scattered access control.

Thus, the company decides it’s high time to do something about that and to simplify the teams’ work (of course, to boost productivity as well!). Consolidating everything into one centralized Jira Cloud environment is the best option. 

 So, how can they do it? 

Step 1: Back up all Jira instances before making any move

Before initiating any changes, the company’s Jira admin team uses GitProtect backup & DR software to create full, immutable backups of each Jira instance. Since the merging companies operate in different time zones and rely heavily on Jira throughout the workday, the admins set up frequent incremental backups to run continuously. This ensures that, at the moment of migration, both historical and newly added data are fully protected. 

Source: GitProtect - How to set up a backup plan for Jira

To further eliminate the risk of data loss, the team implements a multi-destination backup strategy. They configure GitProtect Cloud as the primary storage and replicate backups to an additional S3-compatible destination as well as to their local infrastructure. In doing so, they fully comply with the 3-2-1 backup rule — storing three copies of data, on two different media, with one stored offsite.

This way, they gain a reliable recovery point for each Jira instance, ensuring that they can roll back instantly if anything goes wrong during the consolidation.

Step 2: Use Deep Clone to consolidate projects

With reliable backups in place, the team is ready to start merging projects from several Jira Cloud instances into one. 

The situation is complex: multiple projects live across different environments, each with its own workflows, field configurations, and issue histories. 

The goal is to unify everything into a single instance, without losing data or disruptions.

The first step in this phase is for the Jira admins to get a clear overview of all custom fields used across the different instances. This helps identify inconsistencies, overlaps, and fields that need to be aligned before migration. It’s a critical step, since mismatched or missing fields are a common source of failure during cross-instance migrations.

It’s also a good opportunity for teams to agree on a unified approach like naming conventions, field usage, and processes so that efforts aren’t just merged technically, but also aligned strategically.

Once the landscape is mapped, the admin team uses Deep Clone for Jira and its Instance Clone feature to begin the transfer. 

Deep Clone is capable of cloning both, global custom fields in company-managed projects, and custom fields in team-managed projects. Making it easier to preserve field data across different configurations.

Once everything is set up, the actual cloning begins. The Deep Clone Project Clone feature moves entire projects from one instance to another.

Whether it’s marketing, product management, or support, each Project Clone can include epics, subtasks, attachments, comments, and can handle up to 100,000 work items per operation. 

Picture caption: Smart Jira Instance Consolidation with Deep Clone for Jira

The feature also supports cloning a project's schemes, which can otherwise be time-consuming to replicate manually, especially when dealing with more complex configurations, such as detailed permission setups.

Workflows with third-party post functions can also be duplicated. While the range of possible post functions is broad, the process has already proven reliable across a wide variety of use cases.

Despite the scale of the migration, the entire process can be completed in a short amount of time. Especially when compared to workarounds like CSV export/import, which are slower, error-prone, and require manual cleanup.

Deep Clone runs the process in the background, provides real-time logs, and can notify the team once the clone is complete. Any minor issues can be reviewed directly in the log, making it easy to resolve mismatches or missed fields without disrupting ongoing service operations.

Clone jobs can also be stopped and resumed, giving teams the flexibility to pause, fix a problem, and continue without starting from scratch.

In the end, what could have taken months manually is completed in a few days or hours. No rollbacks are needed, and all issue data arrives in the target instance fully intact.

And just in case, the backup is still there, providing peace of mind if anything unexpected comes up.

Step 3: Validate and restore if needed

After each project consolidation, the team performs validation checks to make sure issue links, data fields, and workflows behave as expected.

If they discover a misconfiguration or broken reference, they can always restore their Jira data from the pre-migration version.

In the end, the company successfully consolidates all three Jira instances into one. The team now benefits from:

• Consolidated project views, centralized reporting, and improved traceability
• Streamlined admin work
• Consistent access controls and compliance oversight
• Reduced licensing and overhead costs

Step 4: Meet compliance and shared responsibility requirements

After a successful migration, it’s critical to back up the newly consolidated Jira organization. With GitProtect’s backup and disaster recovery solution for Jira, the organization ensures ongoing protection for its Jira environment… not just before the migration, but every day after.

This proactive security approach enables the company to meet both regulatory and platform-side shared responsibility model requirements. While Atlassian secures the platform infrastructure, the responsibility for data, including issue history, projects, attachments, etc., lies with the customer.

With GitProtect in place, the company can:

• Demonstrate backup and recovery readiness to meet standards like ISO 27001, GDPR, SOC 2, and NIS2.
• Retain data long-term to support audit trails, internal policies, or legal hold requests (GitProtect provides unlimited retention).
• Monitor and report on backup status through compliance dashboards, audit logs, and SLA tracking.
• Ensure quick recovery in case of accidental deletion, service outage, or ransomware attack, maintaining business continuity and compliance.

 

Source: GitProtect - Data-driven dashboards

By establishing a robust backup policy post-migration, the organization not only future-proofs its data, but it also aligns with best practices in SaaS security and takes control of its responsibilities under the Cloud Shared Responsibility Model.

Final thoughts

Consolidating your Jira instances is a smart move for performance, oversight, and team collaboration. But it’s also a high-stakes operation. Without the right tools, you risk data loss, configuration errors, and wasted time.

With GitProtect’s disaster recovery and Deep Clone’s powerful consolidation capabilities, Jira admins can confidently plan and execute merging of projects even across instances with less risk and more control. It’s the kind of stack that makes complex administration feel easy.

And, as you see in the use case, thanks to the combined power of GitProtect and Deep Clone, the migration can be fast, safe, and doesn’t disrupt ongoing work.

This article was written in collaboration between codefortynine and GitProtect.

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