hello out there,

we've been doing that sort of thing in bolivia, argentina and venezuela. we stayed away for ABOUT A YEAR each time so the custom paper for the bikes was far out of validity time.
we found different ways to avoid trouble according to this situation:
1) leave the bike in one of the tax-free-border-twin-towns that occur occasionally in south america. for example: corumba/puerto suarez (brazil/bolivia), cucuta/san antonio (colombia/venezuela), foz do iguacu/ciudad del este (brazil/paraguay). it's easy to get your bike officially stamped out there (without leaving the country) and to leave the bike in town forever - if you find someone to take care of it...
2) forget the customs paper and leave the country via a custom-free border post! for example uyuni/ bolivia. a) go to the immigration, stamp yourself out (don't talk about riding a bike). b) leave the country via one of the desert borders west to chile (for ex.: hita cajones / southwest corner).
another option in bolivia: puerto acosta, east edge of lake titicaca to peru, same procedure.
3) leave the bike anywhere in the country (but preferably close to a border) and see what happens if the people there see your expired customs paper. we did this one time in argentina and - surprise - the custom guys did'nt recognize the dates at all...
( this option is probably a bad choice in countries like honduras, as long as you don't want to find yourself paying a 1000$ "fine" ;-) )

if you only stay away for two weeks, your customs paper will be valid anyway after your return and you are very unlikely to have problems anywhere in south america.

good luck to everyone