Correct, every subsite at WP multisite has its own options table db_prefix + blog_id + ‘options’. So we have to make select against every wp_i_options table for every subsite.
uninstall.php is executed inside WP only when you delete plugin at “Plugins” page by click at the ‘Delete’ link. I offered to look at the code to get the idea, where URE stores its data.
Do you see any roles at subsites? Just to check lost you them or no after db prefix change.
I suppose that you have access to “Network admin->Plugins”. So you can network deactivate “User Role Editor Pro”. Click ‘Delete’ under its row after that to fully delete User Role Editor Pro.
1st, try to network deactivate/activate back User Role Editor Pro. Plugin tries to restore its own user capabilities at activation in case they are lost.