Now my question is: when I put the microSD back in the phone and try to sync again after I make changes to my library, will musicbee recognize the the previously synced files? Or will it try to resync because the path to the card has changed?
When syncing files MB looks at filename and date modified. So if you made changes to the files after they were synced, the newly modified files would sync again. Are you aware that there's a preview button which can/should be used before starting the actual sync?
In addition, there's a WiFi Sync app on the play store for MB and Android phones which is even faster than a wired sync. Although it's probably not as fast as syncing to the SD card while it's in your PC. I would do the first (major) sync directly to the card in the PC and then updates (new albums, changes, etc) through WiFi.
I will add that the WiFi app is currently having some issues with Android OS 11. Search this section of the forum to read about them.