OK, I have tested this a little bit.
I am using Cannon Fodder ADF (cr FLT, F load- save FLT - t +4 PDX) version which is recognized by FS-UAE Launcher.
Started game, played first mission through
From mainmenu, selected Save
Clicked FORMAT
switched SAVE DISK to drive
after format, saved game
Closed FS-UAE
Started FS-UAE again via fs-uae launcher with same configuration, and loaded game (inserted SAVE DISK when asked)
Worked perfectly
Are you using FS-UAE Launcher and automatically detected game configurations? If you use manual configurations, you must remember that by default FS-UAE does not ever write anything to original disk images, but uses overlay files instead (see
https://fs-uae.net/floppy-images).
It basically means that overlay files are stored per configuration basis. If you save something to your own save disk, and then copy the adf file to another computer, or use same save disk with different configuation, it will not show previous saved data. Instead, all changes are saved under Documents/FS-UAE/Save States
If you are going to use manual configurations, it might be good idea to disable save game overlays (or enablw writable_floppy_images). However, if you are going to use FS-UAE Launcher automatic game profiles, you should not do that.