Jan Rezab...let me give you some advice...
Do not try to use app email to archive at this time. I had seen other posts regarding users having large email accounts with Gmail... So i considered that my issues was to export (download to my hard drive and store in my server) old emails.
Well, I just lost one year worth of emails, 2012 completely gone! Hopefully there are no law suits coming my way!
I suggest making a label in Gmail for your older emails... then don't show that label the mail app, this will reduce the syncing required. If you need an old email then just use gmail to get to it... at least till they fix this.
Also don't use Mail app to move your mail around, this is how i lost my 2012 emails, they looked like they were moved and then I ended up exporting an empty mailbox and it feels that my mail is now in limbo...
Best,
-G