Ask the player for a breakdown of what was gained when
Assuming you are in a game that cares about accounting for every skill point, they should already have such a breakdown, because it is the only way to correctly produce the character in the first place. If they haven’t done so, they should. If they have, it should be no problem to give it to you.
You can then follow the sequence of level-ups and acquisitions of items and other features to calculate their skill points gained and spent.
Or houserule the problem away
This is an immense amount of work and bookkeeping and accounting, for almost-literally no benefit to the game. Skill points are just not that valuable; they should not consume so much effort. It’s one thing to spend a lot of effort building the important parts of your character, but quite another to do it on trivialities.
It’s also easily fixed: make Intelligence gains retroactively grant skill points. Then you no longer have to worry about when Intelligence went up.
You could go farther, and also eliminate the doubled cost of cross-class skill points, or make that work on the same “once a class skill, always a class skill,” principle that the skill rank maximum does.
You might recognize these changes as being quite similar to what Pathfinder does. They got these ideas from houserule that had been common in 3.5e for years prior to Pathfinder. Ideas like these have been very, very widely used, for the obvious reason that the official rules are complicated, fiddly, and in no way worth it. This is some very well-tested stuff, and I can basically guarantee it will improve your game.
While you’re at it, consolidating the skill list is another thing Pathfinder did that was already widely done as a houserule. In fact, most tables in my experience went further than Paizo did—in 1e. In 2e they pared things down even more. Another thing all but certain to improve your game.