You don't explain the scope of subfloor replacement you're attempting or how 'deep' you've mined into the structure so far to inspect it... Pictures really help get you the exact answers you need!
Which came first, the unsealed gap or the soft flooring?
This is a classic 'Chicken & the Egg' area... Over time when water softens the plywood and/or damages nuts, bolts & washers; the dreaded wood dry-rot allows the flooring to be compressed or outright broken away thereby allowing the frame to droop which opens the gap (wider?) that you're showing us now.
Be very careful you have the cause well repaired, window & window frame gaskets, tail lights, even roof details ie: vents, segment seams, or since the previous storage area may not have been level anything up hill from the water damage. Problems flow downhill!
Honestly I have not worked on such a new Airstream but the best sealing method on older models is to remove the trim band and start the weather proofing directly at the rivets and sheet seams which that trim covers. Once that is accomplished then reinstall the trim with it somewhat bedded in caulk and seal the top/bottom seams from the outside.
Which caulk to use? I am sure someone will have favorites, either singularly or in combination - Sika-flex, Tremco/vulkem, Parbond, Alcoa gutter seal....
Anyhow, that gap being enlarged usually flags deeper problems..