I was able to reproduce this exact problem. Instead of a node_modules folder, I have a *lot* of files in several shares. The repeatable test case was to remove the folder from Resilio Sync, wipe the folder from the drive, create a new one, then sync again. Repeatedly failed. I'm using the Linux (amd64) version, both 2.5.6-1 and 2.5.7-1. Didn't change when I removed the folder and added it again. Downgrading to 2.5.5-1 worked for me. The package I used is here:
http://linux-packages.resilio.com/resilio-sync/deb/pool/non-free/r/resilio-sync/resilio-sync_2.5.5-1_amd64.deb
I wouldn't give up with this software. For instance, one of my many large folders is 77 gigs consumed by 72k files. I've got bigger ones that I sync elsewhere as well and ones with far more files. One of the shares is nearly 200 gigs, another has 200k files. Typically there's no snag. I believe that there's a bug that was introduced with version 2.5.6.