I would like this automation to overwrite the FixVersion field on an issue based on a cloned issue's FixVersion, but for some reason, if the destination issue already has a FixVersion it doesn't overwrite it. What am I missing here?
Then: Edit issue...
Ah... I see some things of note:
Please note the scheduled issues returned (in the PM project) and the branch on linked issues returned (in at least the WPEMEA project). Is this a project-level or a global/multi-project rule? If it is project level this will only process items within the scope of the project where it runs. What is your intent of issues to update: project or instance scope?
And...if this is multi-project, the versions are specific to a project. So you would need to confirm their existence in the target project in order to assign the values (duplicate version names but different instances by project). I wonder why that doesn't show as an error in rule execution...
And...note how the schedule returns more than 100 issues? I believe rule execution is limited to 100 issues from a JQL, branch, LookupIssues, etc. If you expect more than 100 issues you may need more criteria to limit the result set (with JQL)...which could require multiple similar rules.
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