It means what it says.
If you are doing "manual" synchronization – instead of say, using "Sync Library" in connection with an Apple Music subscription or iTunes Match subscription, that means that your iPhone (or iPad or iPod)'s Music library will reflect some selection of music on a Mac or a Windows PC.
You can only synchronize your iPhone's (or iPad's or iPod's) music library against one computer library at a time … so if you synchronize your iPhone against computer A, and then synchronize it against computer B, all of the music loaded onto the iPhone by computer A will be deleted from the iPhone. The same is true if you synchronize against Music library #1 on computer A, and then synchronize against Music library #2 on computer A.
It would appear that the Mac thinks (correctly or incorrectly) that you are synchronizing your iPhone against a new library. So it is warning you that if you proceed, all of the music now on your iPhone will be erased – in favor of the new selection.