How can I transfer inventory available but not on hand? I have a positive in one bin and a negative in the other bin. I ignore "Lot not available" with a script. Could of sworn this used to work.

You likely had a transaction changed or deleted. You'll need to correct the transaction or perform an inventory adjustment matching the attributes of the negative inventory.

I created the negative inventory myself. We can't enter the consumption as fast as we ship. If I have -1000 in one bin and 1000 in another bin can I ship it?

Likely not. NetSuite is a perpetual inventory system and does not support negative inventory if you have inventory attributes (lot, bin, inv status, etc)

Are there any settings that would affect this because it was working last week?