Jira's javascript libraries and frameworks change frequently and quite a lot. It's always well worth avoiding the use of javascript whenever you can.
You are going to need to rewrite the scripts to work with the new version. It might be minor tweaks for some, it might be starting again from scratch. I'd strongly recommend re-evaluating every one before you start to see if you could replace it with something that does the job properly, or discard it as not much use in the first place. (Especially security related ones, as Javascript is not able to do security at all)
However, all you've told us so far is "it doesn't work" - we'll need more detail...
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