Do you book in your MDE app/account? Or while in the park? I’ve read that if you book anything before 4, it’ll delete another day’s FastPasses in your account.
You book FPs as you normally do - on the app, on your computer, whatever your preferred method of choice. If you have no other FPs pre-booked that day, you can pre-book FPs on your MNSSHP day at 60 days out if staying at an eligible resort, 30 days if not.
Booking a FP before 4 doesn’t cause it to delete FPs.
From time to time DISers will report receiving an email that they have too many FPs booked relative to the ticket media in their profile and that their last day of booked FPs will be cancelled if not addressed. Exactly who and why some get this warning is a mystery, despite a few theories around.
BUT, reports of this happening are rather rare. It is possible and every year it seems to happen to a few, but I don’t personally think it’s something to worry too much about unless you receive a warning email.
There is the same FP booking situation with Disney After Hours tickets and they’ve been doing a ton more of those events this year - I haven’t seen any warning reports (I run the three threads covering those events and this same topic gets lots of discussion). Granted the DIS is a small sample size, but still.
So my advice, book your FPs, monitor any emails you may receive from Disney leading up to your trip (if any), and otherwise don’t worry about it.