Thanks to GOG support I found a solution to transfer pilots to The Secret Missions even if you've been playing the new version of Wing Commander 1. The secret: your saves aren't actually in GAMEDAT, they are in cloud_saves. So, TRANSFER.EXE doesn't see your saves.

1. Make a copy of the cloud_saves\GAMEDAT directory.
2. In GOG Galaxy go to Manage Installation > Configure
3. There should be 2 versions: "Version 1.0" is the new, and "Version" is the old. Choose the old "Version".
3.b. I also turn off cloud saves. I don't know if it's needed or not, but for our purposes it's best if Galaxy won't mess with our saves.
4. After you press okay, a progress bar will appear. After it's done, there will be a nice, tempting "UPDATE" button. DON'T touch that button. That would update the game to the new version.
5. Overwrite the GAMEDAT directory with the backup you made from the cloud_saves\GAMEDAT directory.
6. Run TRANSFER.EXE from DosBox. Now the savegames should be sleeping in the bunk beds.

This method just worked for me, so I'm afraid to touch anything, not to ruin it, but you might went to experiment with another method:

1. Overwrite GAMEDAT with cloud_saves\GAMEDAT. (Just copy over it.)
2. Run TRANSFER.EXE and transfer the pilot to The Secret Missions.
3. Overwirte cloud_saves\GAMEDAT with GAMEDAT.

I have no idea if this second method works or not, but might be worth a try. If it doesn't work, try turning off cloud saves, but keep Version 1.0.

I hope this helps.

UPDATE:

I managed to transfer saves to Secret Missions 2: Crusade and Wing Commnander 2.

TRANS2.EXE works the same way as TRANSFER.EXE.

To transfer WC1 characters to WC2 the following method worked for me:

1. Make a copy of the WC1 GAMEDAT directory in a place with a simple path you can remember.
2. In GOG Galaxy change the Wing Commander 2 version to the older version, similarly to above steps #2-4. (I don't know if this is necessary.)
3. Run DosBox.
4. Mount the path of the GAMEDAT directory you saved in step 1. You need to remember the mounted path of the GAMEDATE directory. (Let's say I copied it to d:\saves\gamedat\ and mounted d:\saves\ as R, then the path will be r:\gamedat)
5. Run Wing Commander 2:
- 5.a. Mount the drive WC2 is installed on (this might be your boot drive, DosBox doesn't like it, but it's fine).
- 5.b. Switch to the directory WC2 is installed in. DosBox shortens directories to 8 letters, so you might have to type things like this: CD goggal~1 ; CD wingco~2 . To find out what directory to change to, I leave a Windows browser open with the entire path (you can get this from GOG Galaxy: Manage Installation > Show folder) and type DIR /P in DosBox to see what directories you can choose from.
- 5.c Type WC2
6. WC2 will run in DosBox. It will be slow, because you're running it with the default settings of DosBox, not the GoG settings. It's fine, we won't play the game. Press ESC, click NEW GAME, press ESC until you see the menu.
7. Choose Transfer character and choose which campaign you want to transfer from.
8. Type in the path as you mounted it. (In the above example it should be r:\gamedat)
9. You should see your savegames with your number of kills. That should help you find the most recent save.