1) is Atahualpa safe to use - ASFAIK yes, there is nothing in any new WP upgrade that has caused it problems, if there is and I can fix it, I'll create a patch. The reason it doesn't show on WP naymore is because they theme review team made a decision two years ago, that all themes MUST use the customizer. It would take a emense amount of time to do that for atahialpa and there is no payback for the effort. (i.e. If I did it and it took me 100-200 hours to do, what would be my benifit?
2) It you truly edited wp-admin/widgets.php and it was empty, I would be very concerned. The three ways I can surmise this could happen are
1 - you didn't actually open that file, you had a typo and opened a new file tattt was empty
2 - an update of wordpress timed out or failled and the file was not created
3 - you may have been hacked.
Had you said you had just updated Atahualpa to version 3.7.24, I would have pointed you to this
thread from back in May of 2015