Now that I've purchased a bigger SD card, in fact, the exact card that comes stock with the phone (just bigger) I'm having the same shitty problems. Every time I add one album, I'm going to have to wait for this garbage to remove everything and re-sync? That takes 4-5 hours, BTW. Yes. 4-5 hours. Jesus Christ! I'm about to put this phone on eBay because of this alone...
Wow, 4-5 hours, that's absurd. Must be the slow access time of the SD card compared to flash memory. I've never had an MP3 player with an SD card, so I can't say for sure, but I suspect the SD card may be treated separately from the flash memory, by MediaMonkey.
That is, does MediaMonkey list them separately on the left column? If so, then you would probably right-click the SD Card in the listing, then Configure Device, etc., just like you did with the Phone itself.
What I would normally do is to create a playlist with a name like "Nexus SD Card". When you do the Configure Device thing for the SD Card, make sure you've selected that playlist under the Playlists tab. That way it will maintain that playlist on the device at all times, updating it when needed, but never erasing and restoring the entire playlist every time.
When you want to add an album or song, you simply add it to the "Nexus SD Card" playlist, and it will be added ONCE, next time you sync. When things are getting removed when you don't want them to be, it's because you haven't selected them to be retained, in the Configure Device area.
If there's a better program for syncing with the Nexus One, maybe someone else out there can suggest one. I'm familiar with MediaMonkey from past use with various MP3 players and iPods, so that's what I'll be using on the N1 when Verizon finally gets it.