HOW PI CALCULATES THE NUMBERS DURING UPDATE

The key in the RPRO PI is the Store Start QTY. The first step is to make sure you have the databases synchronized. So we recommend initializing the remote about 2 to 3 days prior to the PI, this syncs the databases. Then the you Press NEW at the store it takes a snap shot of the quantities on hand at that moment and freezes them. This is the base comparison point for the update.
The Second Major Key is EVERYTHING MUST BE COUNTED WHILE THE STORE IS CLOSED. If inventory moves during a PI and is sold received or transferred then the comparisons will be flawed and you inventory will be skewed by double that amount of the moving product. The PI COUNTS are Stored in the STORE PHYS column the second pint of comparison
Answering your question about transfers during a PI as long as EVERYTHING IS COUNTED WHILE THE STORE IS CLOSED AND NO PRODUCT MOVED. You can do transfers, there is a 3rd point of comparison for update and that is the QTY COLUMN. This column is what you currently have on hand. So it reflects sales receiving and transfers.
IE
ITEM 1 STORE START STORE PHYS QTY
10 8 9

in the above scenario you press start and it freezes 10 in store start you count 8 so that is a difference of 2 but then you transfer 1 out AFTER THE STORE HAS BEEN COUNTED, now the QTY goes to 9. The way the update works is it takes the store start and store phys and subtracts the difference between the two to come up with the new on hand, but it also looks at the difference between the QTY and STORE START and factors that in as well. So our new count with sales receiving and transfers taken into account is
10-2=8-1=7

REMEMBER, EVERYTHING MUST BE COUNTED WHILE THE STORE IS CLOSED or the PI will not be accurate.

I have also attached our how to do a phys in v8 which outlines all these steps.

Hope that answers your question