Help with registry clean up

Hi I have a problem with cleaning up after a portable program run. The situation is thus, I have several programs created by let's say Company which might be run at the same time creating a situation such as below:

HKCU\Software\Company\Program1
HKCU\Software\Company\Program2


as such I cannot use

[RegistryCleanUpForce] nor backup
1=HKCU\Software\Company

as this will delete the other program running.

So that leaves me with running
[RegistryCleanupIfEmpty]
1=HKCU\Software\Company

which does not work due to the fact that the "HKCU\Software\Company" will have a key

{Default}=REG_SZ:{value not set}

I need some way to remove that and run RegistryCleanIfEmpty.