How is Budgeted shrink calculated for location that had physical inventory in same period HTD table

I understand that inter-stock take shrink divided by inter-stock take sales is your shrink percentage and this process of calculating percentage is done through HTD batch. What if physical inventory is done during same period when HTD is due to run during month-end and all inter-stock take shrink and sales is reset to zero and only has cumulative information for post stock count information. How will then BS % be calculated (as data in IST isnt sufficient)? Does it take actual inventory result into account? if it does, where does this batch get sales data (as inter-stock sales has been