We need your save files to check what is wrong, the information is great to have to know what happend but without the save its like nearly imposible to see/re-made the bug .
just Zip the saves and upload them here.
Play game up to where the Transformation quest says "See if Edgar has an outfit available".
Then drop off the familiar in the MC's room in the tower.
Go ask Edgar about the outfit. Since Edgar needs to see the familiar for measurements, the familiar pulls herself out of the ether and shows herself to Edgar. She now exists in the MC's room and with the MC at Edgar's. Walking into the MC's room transforms the one with the MC before the MC can reach the only already in the room.
I didn't ask for the bug to be fixed, I just pointed it out to the forum to show that it is funny.
You don't ask for my save, just told me I had to give it to you. That kind of inclines me not to give it to you, especially since I detailed how it can be duplicated in my first post, reiterated again here for clarity. If you can't duplicate it, then it really isn't much to be concerned about. But I believe it can duplicated each and every time you follow the above steps. Kind of annoyed that you called that "impossible to see/re-made" without even thinking about what I said.
Ask yourself, what is Edgar's response to the MC asking for the familiar's outfit. Find yourself the answer and you will see how that duplicates the familiar if she is not with the MC.