Hi,
First of all Moodle is nothing to do with Bootstrap.
Moodle has many themes, some which have been incorporated into the Moodle/theme directory and were created using Bootstrap 2.3.2. These themes are a new breed of themes and in some respects are still prototypes, but are as of Moodle 2.7 the default themes for Moodle.
The only Bootstrap folder in Moodle 2.8.1 can be found in Moodle/theme/bootstrapbase/less/bootstrap. This folder contains ALL the necesary styles for Moodle boostrapbase themes.
However, that aside, you did not say what version of Moodle your institution upgraded from. If 2.3 or 2.4. then the Bootstrap folder you are talking about must be the Bootstrap theme by Bas Brand. If that is empty then the theme you are seeing is Clean theme which is the default theme in Moodle 2.8.1.
Hope this helps?
Mary
PS: Edited to add more info:
This is what the files system of Moodle 2.8 looks like:
https://github.com/moodle/moodle/tree/MOODLE_28_STABLE
This is the file structure of the theme directory:
https://github.com/moodle/moodle/tree/MOODLE_28_STABLE/theme
And this is Moodle Bootstrapbase theme:
https://github.com/moodle/moodle/tree/MOODLE_28_STABLE/theme/bootstrapbase
Hope this helps?
Mary