Are there any guides listing common know issues/to be aware off when migrating one jira instance to another?
That's far too open a question to answer in a guide. The variations in your systems are practically infinite, so there's no way to write such a thing.
Work through a test run of https://confluence.atlassian.com/adminjiraserver071/migrating-jira-applications-to-another-server-802592269.html
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