Hi there and thanks for your reply!
I first noticed this behaviour the following way: I started using this setup to synchronize my World of Warcraft addons between machines. Machine A is my home machine, machine C is at my parents home, where I visit about once a month. I started noticing that addons I installed on my home machine (A) where gone when I returned from my parents house (I never realized they were missing at my parents, since I am not really doing much there). I reinstalled them at home and forgot about it. When I came back from my parents the next time, same thing happened. I went there this weekend and had a look at syncthing there. I use SyncTrayzor which has a “Global Changes” feature where you can see the last changes it encountered. And it read "CASTLE (name of the machine at my parents) deleted ", so I am sure it is in fact machine C who is deleting the stuff.
The machines have been in sync in the beginning, since I copied the addon folder manually from C to A when I got my new home computer.
I have no problem resetting and starting over if my current setup is screwed up. Was my way to configure things (every computer shares with every other) the right one? Or should it rather be A and C sync with B (the server) but not with each other? I am using syncthing for other stuff too but for now with a simple two-machine setup. I’d like to sort this one out before using it in a more complex way with important stuff 