having a hand on the system I could probably find a root cause. But doing this just on a small portion of text information will probably result in a thread with more than a hundred replies and days.
SAP Support can access your system.
You may need to contact them anyway for the deletion on transfer orders. There used to be an instruction in OSS note 1454038 - How to Cancel / Confirm a transfer order when the delivery has been deleted
But this note is currently not released, maybe it gets reworked. You may ask to get it released for you.
The negative stock has to be zeroed by creating a manual TO with LT01 and movement 999 by moving the material from your warehouse bins to the interim storage bin with the negative quantity.