I just did a key update and found that my polybagged with cards versions of X Force #1 were removed as minor keys, while my cover A copies remained minor keys. My understanding is that these were all 1st prints, just polybagged with cards. If that’s the case, I believe they should remain minor keys.
My understanding is that a while back the editors decided that a bagged edition is not a variant. So they have been removing those bagged versions as they find them.
Right now, there are only five indexed: the direct, the newsstand, the negative UPC, the Australian and the 2nd printing.
My guess is that your copies are linked to variant G, H, I, etc. They lost their key status because your copies are no longer linked to an official entry in the Core.
So one option is to relink all of your bagged editions to the “A”, and then use the notes or the variant description to indicate which card it has and/or that it is still polybagged.
It’s what @Reinharc said. They were merged to the book that’s inside the polybag. The cards are what is different, not the book. Which is why the decision has been made to remove them from Core. You can still keep these entries in your database if you want to.