A few recommended articles to read on registry cleaners:
Registry cleaners are not supported by Microsoft
"Microsoft cannot guarantee that problems resulting from the use of a registry cleaning utility can be solved. Issues caused by these utilities may not be repairable and lost data may not be recoverable"
In most cases regardless of which Registry Cleaning tool you use it's not going to outright break Windows from booting or running. Normally the damage done is rarely seen or even attributed to the cleaning. How it can sometimes manifest itself is with an application simply not behaving as it used to, a program feature that no longer launches. In some cases on a computer with detailed auditing enabled it can show errors that were not there prior to the cleaning, but again these are typically things that would be nearly impossible to know after the fact what caused it.
The bottom line is WHY are you cleaning the Registry? The system can typically read through the entire Registry in under a minute, but that is not how software reads, writes to the Registry. It makes a specific call to a location where it expects its configuration to be or where it needs to possibly interface with other COM objects to complete an operation and can typically make that read in milliseconds. Reading all the keys for my HKCU hive took 249 ms with a total of 21047 keys. So how is removing a dozen or a few dozen going to really help speed up my computer?
If you can show proof positive 100% that some value in the Registry is actually causing an issue then change or remove THAT entry. Not hundreds or dozens of entries because someone that has been programming for a few years now somehow feels they or their team know the Billions of possible values and every single one that is good or bad and can automate fixing it. Sorry but I call
BS, no one knows every single entry and what it means let alone if its good or bad.