I haven't used it with very large files (100mb pdf is the largest thus far), but I've had problems with making sure every client has the same version. SyncThing doesn't sync with those using a different major version, and some SyncThing wrappers aren't as good as others with keeping itself up-to-date.

This resulted in a merge conflict with a large KeePassX db file x_x

I haven't had any issues with SyncThing so far, other than the initial setup faff! I haven't had to deal with any horrible merges, and as long as you take frequent snapshots you should be able to recover if the worst happens.