One would have to inspect the code of the customized theme to see what might be the problem. It is possible that the customized template was replaced with new upgrade to Moodle if the customized template was actually one of the default templates (customized template name the same as those normally installed by Moodle - see listing below).
Temporary fix, however, is to *go directly to* via URL:
Site Admin -> Appearance -> Themes -> Theme Selector.
Example: http://site/moodle/theme/index.php
Replace [site] with your URL and [moodle] with your installation directory.
You should be prompted to login. After logging on, you should be at the Theme Selector page.
The current default, is the one that has a 'box' surrounding the info for the template. The screen shot of the template may/may not be accurate (depends upon IF the former Moodle Admin created a screen shot of it or not).
Do note the name of the theme as that directly relates where to find the files for the customized theme: /moodle/theme/[name_of_theme]
Select the default theme to something that has NOT be customized. You will loose customizations, naturally, but should be able to navigate around and your site is 'useable' (maybe) for others - although, here again, some 'features' might be missing.
In your /moodle/theme/ directory, the themes installed with Moodle are:
chameleon, cornflower, custom_corners, formal_white, metal. oceanblue, orangewhite, orangewhitepda, standard, standardblue,
standardgreen, standardlogo, standardized, standardwhite, and wood
Many of the settings for a 1.9 Moodle are in a table called mdl_config
A value labeled theme contains the name of the default theme chosen.
It should be possible to 'hard wire' that in the config.php file of your site.
$CFG->theme = 'standardwhite';
Where the value is one of the installed theme names (listed above).
Am not a designer so can't help with the customization 'fixes'.
'spirit of sharing', Ken