What are the registry database disadvantages using a registry cleaner?

A problem associated with registry cleaners is that some of them do not rate the severity of errors, and most that are able to do this incorrectly classify errors as critical, with diminutive reasons in support - a contemporary form of snake oil.

What are the limitations of Registry Cleaners?

Critics often claim that there is no authentic way of knowing whether a third party application has an invalid key, redundant information or not.

Weakly developed registry cleaners may certainly not identify whether a particular key is still in use by Windows or what dire consequences it may have on being removed.

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The abovementioned flaw in Registry Cleaners create some worrisome situation such as malfunctioning of system, loss of functionality and accessing Microsofts application compatibility updates to prevent harmful Registry Cleaners.

Registry Cleaners have their own limitations for instance they cannot correct scenarios like undeletable registry keys owing to insertion of null characters in their names. Some specialized tools such as Sysinternals (now Microsoft) and RegDelNull utility can perform this task.

Potential to Recover:

Registry Cleaner could not repair those Registry hives which couldnt be mounted by the system.

Despite all these problems, a corrupt registry can be recovered in several ways supported by Microsoft. For instance Automated System Recovery by using System Restore or by running setup from the Last Known Good boot menu.

Malware elimination:

Nevertheless, it can recover a corrupt registry in numerous ways backed by Microsoft; for example, Automated System Recovery, from a Last Known Good configuration, by enabling the setup to re-run or by deploying System Restore.

Registry Cleaners fail to detect or delete Registry entries linked with a rootkit that can conceal this information from other processes.

A specialized tool is needed to compare the results of Registry APIs with the raw underlying Registry storage.

Functioning of Registry Cleaners in case of application virtualization:

Registry Cleaners could not remove those Registry entries which are written for a virtualized application.