No, I haven't had a deleted master page item return on it's own, but it would if you reapply the master to the body page.
That said, I agree with Adobe support rep—take a minute to create a new, linked master for the opening page of the book. You need it for all the chapter openings anyway.
Troubleshooting first, which you may have already done:
Does the item have dotted lines indicating it is still on the master? Solid means it is on the page.
Is it only on one page or more than one?
Can you Cmd + Shift + Click it to select it?
What letter(s) appear in the Pages panel in the corner of the page? Does that match the Master you applied?
If you create another page based on the same Master, does the item appear?
Is the Master based on another Master?
What happens if you Remove All Local Overrides from the Master Pages?
Oh, I just read your post more carefully. It sounds as if you are trying to use one Master for two layouts. The best practice is to use two masters in your case. One for the main pages, one for the first page. Create a New Master with a parent/child relationship so if you change the parent, the child changes. Apply the First Page Master to the first page of each chapter.
It is never a good idea to make overrides on a page from the master. Make a new master depending on the old master and apply this to the pages. Overriding master elements on pages, not on masters, causes a lot of problems, like reappearing when reapplying a master, but also with EPUB export and it makes it impossible to export PDF/UA where a strict separation between master and page objects is required.
With EPUBs and PDF/UA master page objects are not part of the reading order, and with several EPUB types all master objects are ignored, as they serve more for decoration and orientation than to be part of the content. It becomes important for people with visual incapabilities to have this separation. For print it is of course not a problem.
I am from InDesign Engineering Team. I am investigating similar issue. It would be great helpif you could share you file where you are seeing this reappearing issue happening.
You can share your file @ email@example.com using dropbox or any file sharing service.
Thanks in Advance.