If I understand your scenario it sounds like:
Player A has 1000
SB posted 1000 and folds
BB posted 2000
If that is the scenario then BB can take 1000 back and then BB and Player A play for the 3000 in the middle.
That's what I understood from the OP as well...
If Someone is all-in for 1K, & it's folded around to the BB (2K), the BB pulls back !K to "match" the all-in, leaving 3K in the pot ....