1. Do a physical inventory and set all user-costed items to zero quantity and zero cost

2. Change the account sets

3. Do an IC adjustment batch to return them to inventory, the adjustment batch will force you to add lot numbers.

I tried this for just one item.  The "Allow lot quantities to be different from the quantity in the entries." box remains greyed out, and prevents me from seeing the Lot Costed account set in the list of available account sets. 

Tried running Day-End processing to see if there is any difference, but still unable to uncheck that box

Found that for step 2 I can simply delete and recreate the item with the correct account set after the quantities and cost are zero'd in the way you said.

I also found that I can uncheck the "Allow lot quantities to be different.." box, by setting ICITEM.LDIFQTYOK to 0. When I do it this way I am able to change from the user-specified account set to the lot costed one without deleting the item. 

(UPDATE ICITEM SET LDIFQTYOK=0 WHERE ITEMNO='XXX')

Is unchecking that box in this way and then changing account set going to cause problems later?   

Also, the items I am working with are already lotted. I'm just changing from an account set that uses User Specified Costing to  an account set that uses Lot Costing. I found that by setting LDIFQTYOK=0, it allows me to change the account set of items that have a non zero quantity/cost to the lot costed account set.  Will this cause errors later?

I don't know, I've never touched that field before.