iTunes - Syncing with or without Manual Manage Music, etc.

OSX 10.11 - iTunes 12.3.1.23 running. I have 5 iPod Classics so I would like to manage my music as I see fit but APPLE keeps futzing with iTunes, adding some functions/features programmers think are cool or are improvements but in actuality take away useful function that should have been left alone.

To wit, my question - if I've previously selected Manually Manage Music, if I go to remove that and let iTunes sync automatically, I'm advised the all existing content will be replaced from my current iTunes. If I haven't selected Manually Manage Music and now select it I get a message I'll have to eject before disconnecting Plus all existing content will be replaced, etc.. Going back and forth on this option seems is confusing because I'm not sure what's going to happen. Why does the entire Library get erased and start all over when syncing? We're talking 16,000 songs on each iPod.

Also, THIS message is shown when I try to apply the change for both the above approaches -

"Music, movies, and TV shows synced to “James's iPod Black 39ZU” from other iTunes libraries will be removed and items will be synced from this iTunes library."

My question here is we're only talking One iTunes library so is this message irrelevant if the iPod(s) in question have previously been synced from this one library?