Hi @dylandawg
Not sure what may be going on there, as the plugin shouldn’t be touching post ID associations at all, just taxonomy and parent columns.

Curious if https://core.trac.ww.wp.xz.cn/ticket/64357 is related, as we do use include as part of our arguments.
Hi I don’t technically know how this plugin work.
I can tell you I moved core tag terms to a custom taxonomy and none of the posts had that term associated to them on the dashboard. They showed up as still having the core tag on the post list (even though the tag didn’t exist any more, it moved the tag not the associations).
So I did the inverse procedure, I moved all terms from the new custom taxonomy back to core tags.
And tried this plugin > https://ww.wp.xz.cn/plugins/term-taxonomy-converter/
I don’t know how they are doing it different than you but that plugin besides moving all tags to custom tax also associated all posts to the moved terms.
You should check it out and see if you wanted.
Hope that helps.
Only “gotcha” I can think of here would be if the new taxonomy is getting successfully and properly associated with the post type of the intended destination.
Looking at that other plugin you brought up, they’re essentially creating matching new entries and updating the posts programmatically to receive the new (but same) terms.