Backflagging is the process of a guild going back and allowing its members to take flags that its already passed. This isn't even nessicarily something old.. just something lower. Like, in the PoP era, a Time guild would have to backflag for members who needed Elemental flags.
Backflagging generally uses alternative methods of flagging. Such as, in PoTime, there is an item you can loot that will flag you for PoTime. Why's this matter? The 85% rule. Most of the guild has it, some need it, they get it for them. Drops off trash. Only half of your Anguish-geared guild has Time flag? Well, do the math. Take all those that have the flag, then fill out the 15% seats to part of those who don't. Next time you do it, there will be more Time flagged, so you can fill out more seats, til everyone has it. There are similar backflags for Dreadspire and all.
Backflagging CAN also refer to going back and having the entire guild redoing everything together, like the posters above mentioned. However, this isn't the real meaning of the word.. just one way its used due to the confusion.