🚀 go-pugleaf

A couple of suggestions: 

I would guess this problem is the result of "cloning" files--creating new ones by duplicating and editting another. All of the items you edit will retain the same IDs they had in the original file. You could probably reduce such problems in the future by cutting those paragraphs from the document and then pasting them back in before editing them, which would assign them new IDs. If there are just a few paragraphs that are causing problems, you can force Frame to renumber them by cutting and pasting. 

If you save each file to MIF, you can open it as text and then search for and remove all of the <Unique #######> statements. Then make sure the <DNextUnique #######> statements in each file specify reasonably random starting numbers. When you convert the file back to document format, all items will be assigned new, consecutive IDs starting with the specified DNextUnique value.