That's a classic symptom of "workflow tables don't match issue tables". It's quite hard to get into that state without broken code/scripts, and your case sounds very odd - the only way I can imagine you'd be able to get there is to have two post-functions that are doing unusual things. One (not the post-function you've removed) is breaking the data. Then the post-function you removed and put back, is (accidentally?) fixing the damage done by the first.
Anyway, cause not withstanding, there are four things you can do. In order of preference that I'd do them:
- Try the "integrity checker" - that explicitly has a module to check for this mismatch and repair it.
- Force a workflow change - copy the workflow scheme and workflow(s) to a new name, check it works, and apply it to the project.
- Force a workflow change - move the affected issues to another project, ideally one with different workflows
- You've already got this one - clone the issues and delete the old ones
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