CCleaner Fails to Recognize Program Paths Using Junctions

We recommend that you don’t regularly use the Registry Cleaner with Windows 10 or 11, only use it if you have a specific problem.

The Registry Cleaner is meant as a tool for fixing things if there is a problem, it is not meant for regular use.

Using any registry cleaner on a Windows 10 or 11 machine can, and will, remove entries that may be needed by modern software - as you have already found.

Using any registry cleaner will not speed up your machine in any way, and only saves a few KB of disc space.
Using a registry cleaner on a healthy machine can even ‘break’ it to the point of requiring a full Windows reinstallation..

Windows 10/11 changes the registry too often to make using any registry cleaner totally safe.
Running any Registry Cleaner regularly can, and does, lead to problems.

For the official Piriform advice on using the CCleaner Registry Cleaner see this:

Here is Microsofts’ advice on using any Registry Cleaner: