Good news! LibLime has made some changes in the way items with a Not for loan status (In Processing, On Order, etc.) are handled at the time of checkout/checkin. Since we migrated to Koha, you have had to manually clear the Not for loan status and then check in new items to trap holds. However, effective immediately you can simply check in your new items to clear the status and trap holds all in one step. The Not for loan status is automatically cleared when items are checked in.
If you attempt to check out items with a Not for loan status, you will still get a message alerting you that the item is Not for loan. You may override the message and check out the item, but the status will not clear upon checkout. It will remain on the item until it is returned to the library and checked in. Upon checkin, the status will clear.
We did not know this change was coming in the last upgrade, and it took a little while to realize that a change had been made. We have confirmed with LibLime that the change was made when they added clarity to the difference between items that are "not for loan" vs. items that are "not for hold" (this was done in response to problems with items incorrectly appearing on the Holds Queue report).