Since the phone syncs with the account on the Pc i don't know how you could avoid removal on the Pc i know on mine if i want to save a Message but Clear my inbox i go to my Gmail on the Pc and i will move the message to a to folder..b33
IIRC it's a setting you make on your on-line gmail account to save a copy of your emails. I have mine set up not to delete the on-line copy if I open it on my Razr Maxx or my computer. About once a day, I log into my on-line account and delete the emails and empty the spam folder.
I think it's under Settings - Forwarding and POP or something such as that. About 1/2 way down the page I tell it to leave a copy on the server. Now, that might only pertain to my computer using Outlook Express, I'm not sure. However, I never delete them from my phone if I think I might want to open it on my computer when I get home. I like to save emails from friends and family on my computer. I also save certain other emails from one reason or another. I don't save things on my phone except maybe temporarily.
Go to the Gmail settings on your computer, then click on FORWARD AND POP/IMAP. Under the POP DOWNLOAD feature, see the option #2 section ("When message are accessed with POP") and select either "keep Gmail's copy in the inbox" or "archive Gmail's copy" - whichever action you prefer.
Sounds like you're wanting to ARCHIVE your messages for later use. Why not use the ARCHIVE tab on your Droid, then go back and clean-up the ARCHIVE folder as you see fit later? Seems to be less complicated...IMHO