In theory ... once all is working well on your v1.3.6 site ...
Backup the database ...
Empty the database on the v1.3.6 site ...
Load a copy of the v1.2.6 site ...
Run the /zc_install on the v1.3.6 site ... and UPGRADE ...
Test things out and write down any changes you need to do such as:
Edit all Payment Modules and write down settings ... remove ... install ... reconfigure ...
Edit all Shipping Modules and write down settings ... remove ... install ... reconfigure ...
Edit all Order Total Modules and write down settings ... remove ... install ... reconfigure ...
Setup your Template ... that got lost on the drop/add of the database tables ...
Setup your side boxes ... those got lost on the drop/add of the database tables ...
You are keeping notes right?
When you think you are done ...
Repeat processes and test your notes and update them ...
Once you have this upgrade down to a science ... and you have tested your site and all is 100% perfect ... then you will be ready to do it for real ...
Take Live site Down for Maintance ...
Backup database ...
Empty v1.3.6 site database ...
Load Live site database ...
Run /zc_install and UPGRADE v1.3.6 site ...
Follow notes and get all happy again ...
Test Test Test ...
Once all is good, you then are moving the Live site to /old_shop and your v1.3.6 where your Live site was example /catalog ...
NOTE: be sure you changed the PATHS ONLY on the 2 configure.php files to the Live Site vs v1.3.6 site ... do NOT change the database as you are now using the v1.3.6 database ... save the old database from the Live site in case of emergency ...
There are many threads on how to do this type of upgrade for the least amount of down time and the safeties to check, perform, etc.
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