I perfectly understand your fear... I am a "keep all the save files at any cost" myself and hearing that the Switch Cloud can accidentally lose part of the save files scares me a lot... i have a lot of hours of playing in a lot of games, and i don't want to lose any of my hard-worked achievement.
That being said, i admit that i don't pay much attention to the "notification" of the Switch while i am using it.
I leave the backup option on auto-backup, with occasional manual backup when i used it in flying mode (mostly for battery and/or travel-without-WiFi reason). Also, all of my game are physical version (i am also afraid of never been able to play a game if it gets retired from the online store), but this should not make any difference...
My guess is that the data about your story progression got somehow corrupted (and replaced with that "starter file" with 0 hours in it) while those about achievement (probably stored on a different "block of memory") was not, and so you get that strange save file...
Did you deleted the save file from the consolle (ie, keeping it only in the Cloud) before all this mess happened?