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what i'ld suggest... a general rule that i like to always follow is to use a test system for everything new. but that does not need to be a full separate system every time.
lets say you have your mailbox and want to try getting new mails from it using fetchmail. first you can use uidl mechanisms to only fefch every mail once and besides that leave them all on the server, but i like it a bit more secure: create a second email adress/account at your mail providers service only for testing. thus you can do whatever you like to to test the mechanisms only without even touching your real inbox (maybe even fill it up with large emails and look how the system reacts, i once had an email account with a cheap provider that deadlocked the inboxes when full..). then when everything is as you want it, switch the account and password (or create another config file for fetchmail) and your're done. every change (not only fetchmail things) could go tested this way before going live with the changes. filtering could be done with procmail for example, but when the mda that is called by procmail somehow exits with success when the email really isn't delivered, then the email might get lost forever depending on the settings of course. so fiddling with new stuff always carries the risk of not fiddling correctly ;-)
have fun !