This should be safe, but you should have a current backup of the database and files anyway. You can (and probably should) install the administration theme in one of the standard themes, so you cannot block yourself from the admin section if you violate your own theme.
If the regions are named different (or are not in the same topic), you may need to move the blocks. Blocks are installed separately for each theme, so just enable the second theme (without setting it by default) and install blocks for this theme. After that, you can set the default theme.
I use a copy of the website to try out the big changes on the website so that I never break the website. This makes it a lot easier and safer, just try things.