What happened here is you’ve overridden the safety measures built in to prevent exactly this kind of situation, and got shot in the foot as the result.
Syncthing creates a folder marker (.stfolder) at the root of a directory it works with. This folder marker isn’t supposed to go anywhere, and if it disappears, Syncthing thinks something unexpected happened and stops. An example may be a folder on a removable device: if the device gets removed, the folder marker can no longer be seen, and that means no work should be done on this folder. When the device gets plugged in again, Syncthing sees the folder marker again and continues operation.
In your case it looks like something happened to your filesystem so that the directory containing your folder started appearing empty to Syncthing. Seeing no files in it, and no folder marker, Syncthing stopped its operation. Then you manually recreated the folder marker, so now Syncthing could see it, but still couldn’t see the files, so Syncthing interpreted the situation in the only possible logical way: there is the directory, it is accessible, but there are no files in it, which means the user (you) has deleted all the files while Syncthing was stopped. So, these files were reported as deleted by you to the other machine, and the other machine acted accordingly.