Nothing more simple :)

a Copy = Ctrl + C / Crtl + V
You work principally in Session A, Session B is your save "SpaceSphip" not filleted! :)
you can have any number of sessions in the same time

Minute 1
Session A : Object O very complex
Session B : Object O copied (from Session A) without Fillet

Minute 2
Session A : Object O Filleted
Session B : Object O - nothing to do

Minute 10 You don't want the Object O with Fillets for any reason so...
Session A : kill the Object O
Session B : Copy Object O (original) for the Session A

Minute 11
Session A : Object O not Filleted (because copied from session B )
Session B : Object O copied without Fillet - nothing to do - or can be receive a new object O modified without fillet you are not oblige to kill the first one...that becomes your data base of unfilleted objects!
etc...
All that avoid to calculate the unfillet (in general impossible in few time) an object at any time of it's conception!
It's very rustic but very efficient!