Your issue here is that you're tracking it wrong. You don't track "uses remaining", you track "uses expended".
If you cast a spell that gives you an ability X/day, and you expend Y number of uses before it expires, then when you recast the spell, you have still used Y uses that day, so the remaining uses is still X-Y.
This works equally for say, cleric turning. If you cast eagle's splendor to give yourself 2 additional turns per day, and then you expend those 2 turns, when you recast eagle's splendor, you've already expended those 2 extra turns. Same reason nightstick stacking doesn't work.
It does get confusing when you start looking at SLAs, because yes, how do you distinguish between each form's SLAs. If you transform into a form that has an SLA at-will, and expend a bunch of uses, then transform into another form where that SLA is limited, are you completely out, because you already used the ability a bunch of times? Luckily, Shapechange does not grant SLAs, it only grants supernatural abilities, which are, for the most part, pretty unique per form.
Right, except the difference is that spells have an active recharge mechanic (ie, you have to DO something to regain them), while all other abilities are simply a "have you used this ability in the past 24 hours" check, and not an active recharge.
I have been trying to find the exact citation that states how the cooldown on abilities works, I remember it being in a super unintuitive rules section, and my table actually houseruled it, because it was actually just too much bookkeeping to keep track of WHEN you cast an ability on each day, so we just set it to recharge at sunrise, because it was easier, and we had a gentleman's agreement to not abuse the game.
It doesn't help that, with 3.5 being so out of date, it's a nightmare trying to look up anything rules related, as it all just defaults to 5e search results.