When using Manage Program to update a Program to "No" based on other programs you select, the entire Program gets updated to "No" regardless of the Programs are selected.
This bug has been corrected and will be part of CMS version 14.5.7 and later.
There is no workaround at this time.
Until the above version is installed, you should not use Manage Programs to update a Program to No based on other programs.
We are working hard to release the above version as soon as possible.