This help page explains how a negative-inventory condition can happen:
As it happens, we're actually updating this aspect of our digital delivery feature right now, as the notifications we send in this scenario can be a bit confusing, as you've seen. Once the buyer's eCheck clears, PayPal sends the order details back to us when they confirm completion of payment; if it turns out that the buyer ordered more codes than you have remaining by the time their check cleared, we won't issue them any codes; instead, we ask them to contact you about the codes they purchased, and we send you a notification about this, so you can decide whether to send them some codes manually or refund their payment, and/or replenish your list of codes for future sales of the product.
The negative-inventory notification is just informing you that more units were ordered than the product's settings say you have on-hand to sell, so you can update those settings accordingly. Don't worry about "making up for" negative inventory; the number of lines that currently remain in your product's codes list at any moment will be the number of units that can be sold until the item becomes unavailable for purchase.
At present we don't have any way to reserve inventory for eChecks to release when the check clears, but that sounds like a good idea if feasible, so we'll put that on the wishlist and look into it.