Fatal error: Cannot redeclare THEMENAME_preprocess_page()
Function names in template.php have to be prefixed with themename_function. At the same time, you cannot have a function declared twice.

bootstrap_agency_preprocess_page() should exist once in bootstrap_agency/template.php, and the other should be bootstrap_agency_minimal_preprocess_page() in bootstrap_agency_minimal/template.php.

If you do not need to do any override, and the one theme is a subtheme, you can simply omit it from template.php. Otherwise, you would need to copy the function code in and amend what you need to amend.