Ok, the simple question is, can you maintain 2 target locks on the same friendly ship? (The way the WE card reads you can, but have to acquire it in 2 different turns. But that is not the "spirit" of the card). If so can you use M9 twice on the same attack with the 2 target locks?

No.

The number of locks you have on a ship is irrelevant to M9-G8's effect, only that you do have a lock on it.

PS: There is a Rules Questions subforum where rules lawyers run free and frolic.

M9-G8 kicks in if you have the enemy locked, not once per target lock. RAW you could indeed lock the same ally twice, but it wouldn't add another re-roll. You could definitely lock an ally and an enemy to help with offence and defence though.

Why would anyone believe this might be possible? Just because Weapons Engineer specifies that you can only have 1 lock per enemy ship?

I hate to break it to you, it doesn't work, regardless of what Weapons Engineer says.

Page 3 of the Rules Reference (emphasis added):

Quote

A ship can acquire a new target lock on a ship that it already has locked; the old target lock is removed.