It shouldn't make a difference once the unit has booted. The initial boot (as you rightly
say) merely calibrates the keyboard AFAIK. I'd be slightly suspicious and keep an eye on
it.
The old 'turn it on and leave it' approach goes right back to the old
K-series and was usually when the battery had failed, but your PC3 is way too new for
that..
The best advice I can give now is : back up EVERYTHING from the unit
NOW. Twice. And double check by opening your save file and checking. You need to do it
anyway before the update but double check as more than once I've accidentally not saved
things right and have lost stuff. Fortunately I was able to go back to a previous
backup.
--------------------
Veni, Vidi, Aesculi
(I came, I saw, I conkered)