"Does CA Form 540NR Line 12 (Total California wages from W-2) need to match up with Schedule A (540NR) Part II, Line 1, Column E (CA wages earned from CA sources as a nonresident)? "
No.
I don't know where the employer got the state wages from - it should have been your pay for one day plus the HSA contributions made WHILE YOU WERE IN CA ON BUSINESS (i.e. one day's worth).
Your employer doesn't actually know all the facets of your return - you are responsible for making the return(s) correct. So if your employer put a funny number in the state Wages box, don't worry about it so long as you can justify the state income that you do end up with.
I assume that this means that your employer over withheld your state tax, so it is important that you file that return.
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