Now that I think about it you are correct, IL runs their own system (FTIP) parallel to NICS, so they would run the checks against their own data after synching with NICS (this includes purchases and new licenses being issued)I think we have two ends of the spectrum here, maybe reversed:
Kentucky runs NICS checks MONTHLY on every carry license holder (talk about bureaucratic churn). Even allowing for that, NICS is still way up.
An ISP press release in 2018 said there were 2,285,990 active FOID cards in Illinois. I doubt the number is lower in 2020. If Illinois ran a federal NICS check on every FOID holder every day that would be roughly 8.5 MILLION NICS checks per MONTH. That's more than the FBI state-by-state stats for the YEAR ending 31 Aug 2020, which show Illinois had 5,179,673 NICS checks for the year. Thus I think we can safely rule out the notion that Illinois is conducing FEDERAL checks on every FOID card holder every day.
Now also in 2018 there were 325,187 CCLs active. Once again I assume the number in 2020 is not smaller. Running a check on every one of them every day would generate 118,693,255 NICS checks in a year, so again I think we can safely bet that Illinois, as lunatic as it is about guns, is not running a NICS check on every CCL or FOID every day.
Who knows what they are doing on a purely state level without accessing the federal data, but I doubt the ISP possesses the computing power that would allow them to run a check everyday on every FOID or even CCL holder.
That said, I have a 5 year old laptop that can compare two tables with over 3 million entries in less than 10 minutes. There's no computing-power reason why they can't run the checks daily. All I can find for confirmation though that is an Auditor-General report that states they check the FOID database against the Mental Health database nightly