Data Transfers · Copy, Move and Sync
What does the “First run for this pair” option do in a two-way sync?
Short answer: It establishes the starting point for a brand-new two-way sync. Tick it only on the first run for a pair of folders; using it again can overwrite one side with the other. Scheduled runs never use it.
It sets the starting point for a new Bidirectional sync. A two-way sync works by comparing each side with how things looked last time; on the very first run there is no "last time", so this option tells it to establish one.
Tick it only once — the first time you sync a particular pair of folders. After that first successful run, leave it off. Ticking it again on a pair that's already set up can overwrite one side with the other.
You'll find it under Advanced options in New Transfer, and it appears only when Bidirectional sync is selected. Scheduled runs never use it, even if you ticked it on the original transfer.
Related: What is Bidirectional sync?