What is the correct procedure to follow after restoring a Mac from a Time Machine Backup?

Hi all,
I did a Time Machine backup of my entire system (Time Machine Backup 1) before bringing my Macbook Pro to the Apple Store to to have it tested.   After the TM backup I wiped the laptop leaving only the OS (Mountain Lion) on it so that I could determine whether the problems with my system were hardware or software related. The computer passed all tests.
After bringing my Macbook home I did a fresh intall of all the software and everything worked fine.  At this point I did another Time Machine backup (in the same location as the previous backup) so that if I ever had problems with my system I could revert to this working backup (Time Machine Backup 2.0).  I used my laptop without issue and created a number of new documents.  I did not transfer the documents from the previous time machine backup (Time Machine Backup 1).  As time progressed I did regular Time Machine backups (backups 2.1 etc.) installed a few new pieces of software and started having system issues again. 
At that point I did another Time Machine backup (in the same location as the previous backups) (Time Machine Backup 3) so that my new documents would be safe.  At this point I could see all of my TM backups in finder.  Then I used Command + R while booting up and restored my system from what I thought was the clean backup (Time Machine Backup 2).  In fact it the TM backup I used was not the correct backup (It was one of the backups between 2.0 and 3 and I needed to go back further).  I was concerned, at this point, because I did not (and still do not) know what type of effect restoring the system from an old Time Machine backup would have on the Time Machine structure going forward  I was unsure whether doing so and having an "old" system backed up might break the structure so I stopped Time Machine from running a new backup. 
When I attempted to look for one of the older versions of the Time Machine backups I discovered that there were no longer any listings for TM backups in their previous location.  In fact, the only thing I could see was one line in the place where the multiple backups were previously.  I took my laptop and NAS (where the TM backups were stored) to the Apple Store and the "genius" said something about the TM backup being "parsed"?  He also described it as a "broken window" and he "sees the broken glass but has no idea how it broke".  He also said "neither he nor anyone at Apple would be able to assist me" and that I'd have to go to a data recovery place.
Fortunately I did use a second drive to backup the original system (Backup 1) but I really don't want to lose the files created ater Backup 2 / prior to Backup 3.
Does anyone know what happened / how I can get my Time Machine backups back without forking out tons of cash?
thanks
John
OS ML 10.8.4, Macbook Pro Retina
Synology DS412 (time machine backup to a file folder)

I actually already checked Pondini's and didn't find the answer.  Any other suggestions?
thanks

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