By items do you mean items issued to the WO with WO-G? If so, each time you use WO-G to issue parts to a repair WO you must set the location from which your parts issue to your inventory location so that parts will pull from there. Otherwise you will just be driving your repair location UOH numbers negative.
 
If you are talking about the repaired items, they process into and then out of your repair location when the invoice is processed. The WO is processed and closed (putting the item into stock) and then the invoice issues the item back out with a repair transaction.
 
If this info does not cover your situation, please share a few more specifics.

The tables for the RMA and SR module start with ISSR and follow the SO module convention: INV, INVL, HINV, etc. You can change the status of RMAs and SRs, but the interrelation of the tables makes it a little tricky. I'm not sure that data normalization is on the to-do list for TAS programmers  
 
One thing that cannot be done is backing out of an SR invoice. Since a complex relationship exists between the invoicing and the Work Orders it really isn't a simple process like it is with regular invoices.  
 
As for the disposition status, that has its own table (ISRMAI), but only mess around in there as a last resort.  
 
My best advice is to connect with Mike (JEMM) who wrote and supports the module. He helped us out a lot.

SO, S&R, RM  
Maybe related because the these modules use the same files.  We have had 2 RMAs somewhat disappear during the disposition stage.    
 
Yesterday we dispositioned a RMA but it did not create a WO.  We went back into the RM and it said it was already closed; but when you look at the line item you can see that line 2 was still "in Transit", even though we did receive it in and disposition it.  It never created a S&R or work order, and we can not reopen it.  The order disspeared from the SR-A module - there is no SR or WO  
 
Today while we dispositioned a new S&R and created a Sales Order for credit we found that the sales order is blank - the customer name appears but the line item is blank  
 
Are these things related?  We use EVO updated 8/4/08