JQL of second script not returning results from first script

I have two scriptrunner script files.  I have two self referencing workflow transitions for each of them.

The first one clones a bunch of issues from a template project and then links them to the current issue.

The second one takes people from a grid and assigns the linked issues based on logic.

These both work when run separate, but when I add them both to the same workflow transition in sequence (clone issues, then assign issues) the assign issues JQL logic doesn't see any of the just cloned issues, so exits without doing anything.

In the first script, I am making sure that I update the indexer, and I've even pushed the last script to the end of the post function list..but still no go.

Is there some sort of temporary state that these newly cloned issues are in that the JQL in the second script can't find them?

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