The command apt-get update merely updates the package database (basically just a list of all the available packages) and doesn't actually change anything. Even if you used the command apt-get upgrade (which will update the packages to the latest available version from the repos), TKLBAM will still be ok with that AFAIK.

Webmin will cause you problems though. Generally the safest way to update anything is via apt. The fix (which I thought the devs were going to implement for the v11.1 release but perhaps not?) was to stop Webmin from being able to update itself (like it sounds like you've done). The pre-installed Webmin is a TKL custom version - the version you can update to from within Webmin is the generic version and that's where the problem lies, updating from custom -> generic is ok, but then when you restore, TKLBAM expects the custom version and breaks Webmin altogether.

In the old 2009.x TKL release you could revert to the custom TKL Webmin by doing apt-get install webmin (or apt-get upgrade) and it would happily revert. Not sure if that's still the case or not.