Mazda6 2012 AT Light and Check Engine Light

Hello.
So heres the story.  I began driving Uber back in Oct '17.  I had to go get a
state inspection to get oked to drive for Uber.  At the shop, found out my axle
boot was ripped.  The guy said he wouldn't charge me if I got the work done
to replace the axle there and not at my usual (very good) mechanic.  So I
begrudgingly agreed.  Wrong move.

I'm now back at my usual shop getting a routine oil change and they find that
the axle seal connecting to the transmission is broken and its been leaking
transmission fluid.  So thankfully, there was a TINY bit of transmission fluid
left and they didn't think the transmission took damage.  But now, after
refilling the transmission fluid and replacing the seal, my AT light and check
engine light are on.  They were not on before I took it in.  And unfortunately,
the master mechanic is on vacation until next week.  The other mechanics
could not figure out why the check engine and AT light are still on.  I'm
thinking maybe the sensors are messed up.

The car seems to drive fine and isn't giving me trouble at all speeds.  
However, I'm still afraid to drive for Uber this week with those lights on.  I'm
thinking it may just be the sensors need to be cleaned or replaced but I really
don't know.  Any thoughts or advice is greatly appreciated.  I am also not
sure if its ok to drive.  I don't want to damage the transmission and create
even more expensive repair than I need. Thanks.