I assume that the problem is to avoid accidentally discarding good mail
in the effort to clean out the in-box. Doing so manually is tedious
and a little risky. You could use rules to eliminate the tedium and
dramatically reduce the risk. Because rules don't run fast, you might
find time for a few rounds of Hearts between runs.
First, turn off incoming mail if you haven't done so already. Back up
any exisiting rules and delete them. Then create a new mail folder to
hold everything you want to keep.
If you want to keep an e-mail, move a copy to the new folder. Then,
create a rule to delete anything that is identical to the e-mail in as
many regards as you think prudent so as to avoid deleting messages that
are not exact duplicates. Run that rule and delete it. Proceed to
next duplicated e-mail and repeat the process described in this
paragraph.
Once you are done, restore rules and folders to their normal states.