For some reason even with steams filecloud synch disabled it still persists on replacing whatever you delete either in or out of game by the next time you start up the game via steam. The only way I have found to keep steam from updating these deletions is just not to use it but its rather annoying. Just an observation that I couldn’t not find a suitable home for.
you are saying that if you create a new custom unit and save it, then later delete that unit, that it comes back regardless of the steam cloud setting? Or does this only apply to the ‘default’ units that come with the game?
I didn’t try to delete the defaults just my personal creations…failures? anyways yes 
I was trying to reproduce this problem last night on a steam install but could not do so. Are you sure this happens in all cases?
For example, if you fire up the game with steam running, go straight to the unit design screen, design a new type of infantry, save them out as name ‘test’ and description ‘test’,
then quit the game (keep steam running)
Then load it again, go to unit design screen click on load design and delete them
Then quit the game
Then load it again, go to design, and load. are they back?
I can’t get it to happen 
I hope this helps. Sorry about the image size about to hit the hay and wanted to reply before then.
First image to show that steam cloud synch is disabled and the files highlighted are to be deleted.
Now they are deleted with same setting still in place.
This is just after it has started up nothing else done, files reappear.
This shows files deleted again and the shortcut on my desktop leads directly to GTB executable located in the steam common folder.
This shows that on launch no files reappear.
So I tried doing this with frapps but well its meant for in game recording not general desktop recording so I went with images instead of downloading a more suitable program.