jQuery_update multisite BOA Drupal breaks

Hi,

I have a custom platform where sites need jQuery_update module enabled for revolution slider. When I do so, I lose many javascript functionalities on the website. e.g. ckeditor disappears, module_filter, expand/collapse functionality lost.

Upon search in the issue queue I found out that module has problem in multisite environment. https://www.drupal.org/node/147256

What is the solution for this problem?

Thanks,