I am running a group in D&D 3.5 and this past Sunday they won a hard fight against some stirges. In winning, they gained enough XP to level up, but during the fight some of them had their consitution scores damaged as a result of the stirges' drain ability. So my question is, with them leveling up, should I have them be using their current constitution scores (which are lowered due to the drain) or their original constitution scores?
The bonus to your maximum life is based on your current Constitution always, not just when leveling up. Even though technically you roll HD+Con each level, losing and gaining Constitution after that point causes you to gain or lose HP equal to your level for each point your Constitution modifier changes.
So it’s easier, in my opinion, to think of it as your HP equals the sum of your HP from HD (whatever you rolled each level, added together), plus \$\left(level \times Con\right)\$. Mathematically, this works out to the same thing. When their Constitution goes back up, they have the same HP they would have if they had rolled with their full Constitution in the first place.
Thus, as long as their Constitution is damaged, their HP is lower than it otherwise would be. When the ability damage is healed, it goes up. Whether you think of this as them gaining their full, usual Constitution bonus, but their maximum HP is reduced by the Constitution damage, or you think of this as them gaining less increase to the maximum HP now, and it will go up later when the Constitution damage is healed, doesn’t really matter.
Changes in a Character's Constitution score modify that Character's Hit Points retroactively. That is to say, gaining constitution and increasing the modifier will cause that character to gain Hit Points equal to their level. A temporary decrease won't have a negative effect in the long run. Depending on the amount of damage, and the character's classes, there is actually a possibility of them gaining Hit Points. However, that is only in certain extreme cases, and you'll never really see that happening unless the DM sets it up themselves.
Temporary CON damage is temporary and should never effect permanent HP changes. If it did, characters would all be casting Bear's Endurance before leveling up. Always use the character's base CON modifier for determining HP from a level up, then apply any temporary CON debufs.
e.g. if a champ is level 3 with 20hp and 12 CON, but has taken 4 CON damage, dropping their max hp to 14, then levels up and rolls a 4, their new base hp total is 25, but they then suffer a temporary penalty of 8 (2(con mod) x 4(lvl)) so their new temp hp total is 17.
This is not really a RAW answer, but it's certainly RAI.