Is it a Kit?

I think you want to look at the cost under that item, after you buy some, rather than in the cost field of the invoice.  That was probably left blank at the time of invoicing.

This is not a kit item.  I wouldn't think the system would let you zero out the cost of the item.   If it is zeroed out at the SO level, inventory will still deduct with the cost on file?

Also, assuming this item was deducted from inventory at a standard cost of $10/each, then a standard unit cost change was done on the item to make it $15/each, is the inventory history file updated to reflect this new cost, or do historical transactions remain at the standard cost the item held at the time it was sold?

This is not a kit item.  I wouldn't think the system would let you zero out the cost of the item.   If it is zeroed out at the SO level, inventory will still deduct with the cost on file?

Also, assuming this item was deducted from inventory at a standard cost of $10/each, then a standard unit cost change was done on the item to make it $15/each, is the inventory history file updated to reflect this new cost, or do historical transactions remain at the standard cost the item held at the time it was sold?

Do you have any add on programs such as Job Ops?

No, but we do have an enhancement that allows for additional levels of customer pricing.  I called customer support about this, and was told that although the item in stock was received in with a cost, if the item was set to Standard Cost and had a Standard Cost of zero at the time of the sale, this could be the cause, however if I run an inventory transaction detail report for the time period in question and select 'use historical cost', the cost at that time was not zero.   I dunno......

What is the valuation method for the item?  You may want to look at the KB article "What is the item cost hierarchy in Sage MAS 90 and Sage MAS 200" - Res ID 638.

I will check it out.  At the time of the questionable transaction(s), the item was standard cost, but has since been changed to lot valuation.