Assuming it is this NavSync script, that doesn't sync files; it is an alternative to Navigation Lock where going up or down in the folder on one side is done in parallel with the folder on the other side (which may be a different location which mirrors the first one).
If you want to synchronize files, see:
If neither of those does what you need, you can also tightly integrate third-party diff/sync tools into Opus:
- External Compare and Merge Tools 2.0
- "Smart" front end for Beyond Compare
- (And several others, but those are the best to start with.)