The presence or lack of e-upgrades in your account has absolutely NO bearing on whether your upgrade will or will not clear prior to airport control. None whatsoever. The automated e-upgrade system is completely independent of everything else, and it has no idea how many upgrades are in your account. (Too, remember that EXPs never burn upgrades for themselves.)
Now, if your upgrade clears and then you try to check in (via OLCI, kiosk, TA, GA, AAngel, etc.) and you do not have enough upgrade credits and are sub-EXP, then the system will stop you and force you to buy upgrades or give up the upgrade. But until the moment of check in, the system doesn't care whether you have enough upgrades or not.