Welcome to the forums. We've always found the folks here to be very helpful, so we're sure you'll get some experienced answers.
Based on your decision to leave the shell on (and your picture not making it into your post), we assume you're replacing a section or two of the floor (not the whole subfloor.) We've restored two Airstreams, but both were earlier models than yours. (We haven't done a 90's trailer.) We have done both with the shell on and both required floor section replacement. First, check that you haven't missed any bolts or screws in the affected area. When you find one, there's probably still another one there someplace. Our '64 was tougher because a large rear section under the bath needed replaced and it was stuck fast. We had to cut, chisel and pry under the C channel to get the wood out in pieces. The '68 was much more forgiving and we pulled the sections out after only two or three rechecks for fasteners. If helpful, our '64 is documented at 64airstream.com and the '68 is documented here at
https://www.airforums.com/forums/f39...er-155180.html , (but probably without subfloor pictures.)
Good luck and enjoy your project,
Roy and Marie