The now free PSTL Tools (I know PSTL Tools is technically redundant, Professional Services Tools Library Tools, but that's how it is commonly referred to) includes an improved Inventory Reconcile tool that only reconciles items that need it. In most cases this is significantly faster than the base tool. How much faster?
I have an example from a client. It's not a perfect benchmark but but in their admittedly slow test environment, it took 24 hours to run the base reconcile and 5 hours to run the PSTL based reconcile. The PSTL reconcile has more volatility in how long it runs because it depends on how many items need to be reconciled.
If you're running in to long IV reconcile times, check out the PSTL based IV reconcile.