There is two parts to this question.
First, fixing the problem causing the empty resolution: Your workflow is missing something to set the resolution. If you look at the built-in default workflow, you will see that all transitions going from a status that means "this still needs attention" to a status meaning "done with this", they all go through a screen that includes the resolution field. This means the users always set a resolution. If you don't want a screen, you can use a post-function to set it instead. (You also want to clear it on "reopen" type transitions). Fix this first, to stop the problem spreading.
Second, the data that is now wrong. Bulk-edit is using the "edit" screen for the issues. The edit screen NEVER includes resolution because when the resolution is on screen, it gets set. If you have it on screen, then every edit will resolve the issue. Which is wrong. You have three options now:
- Reopen and then re-close the issues, setting the resolution (as you have fixed the workflow as above)
- Add a transition to the workflow that goes back to the same status, and has either the resolution screen or a post-function to set the resolution (I usually make it an admin only transition too), and use bulk-edit to perform the transition
- At a quiet time, kick your users off the system, add "resolution" to the edit screen, do the bulk edit, then remove the field again
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