5.6.0.1 update issues

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I'm learning the ropes so bear with me.

I decided to repost this topic as I don't find the ongoing discussions helpful at this point.

I'm a bit wigged out about updating until I find out more. When I updated from the 5.5.2.1 got a warning somewhat similar to
http://www.concrete5.org/community/forums/installation/update-to-5....
-ending with a notation for line 53.

Only access I had to site was through ftp, and restored by changing line in config/site.php back to 5.5.2.1.

updated a new site for my wife went ok, site new and minimal, mine has had some customizations, so...

Question boils down to- how can I check site for problems before attempting this again. Had backed up database but don't want to lose files and filestructures. Reinstalling will provide new questions I'd like to hold off...

Thanks anyone.

Eulalia