I mount D:\ to C:\D to trick cc leaner into scanning both my partitions, but at some point during the cleaning process, it deletes the mount.
I have copied folders from C:\ to D:\,
and replaced the original folders with folder junctions and never suffered any problem.
CCleaner should not realise you were tricking it so should not try to punish you.
There are various ways of mounting D:\ to C:\D
Perhaps you should try a different way.
Be careful how you fool CCleaner and Windows.
Deleting a Mount Point is easy to remedy.
Secure Erasing the contents of the Mount Point destination is a different world of pain and hurt.
I do not think a default installation of CCleaner would produce your effect,
but your loss could be due to :-
an "Include" ;
or a corrupted version of either Winapp2.ini;
or a supplementary cleaning product that shall remain nameless