I have an upper level assembly with a rebuild mark on itself and one child assembly that won't go away.
In trouble shooting - I've deleted everything from the hierarchy to try to narrow the problem. I'm left with just the two assemblies - no parts/sketches/equations/folders/mates/external references/etc. Nothing. See screenshot.
Take the child assembly and open it by itself - no Rebuild Mark.
Take that child assembly and put it in a new assembly - Rebuild Mark shows up.
Add a 2nd instance of the child to the upper assembly - both children now show the Rebuild Mark.
Save As on the child assembly - still shows the Rebuild Mark in the upper level.
Save As on the child assembly and inserting into a new assembly - Rebuild Mark shows up.
Posting this here rather than in the API section as it seems more of a bug - but if there is an API function that would help I'm all for it.