That is not correct. The files will not be regenerated. Files in that folder are custom checks, which you implemented and will be gone, if deleted. In the linked thread they overrode built-in checks, which is why deleting them solved the issue.
The problem here is WMI. This Windows component is known for poor performance and random timeouts. You could tweak a timeout setting for the agent, but even then, the issue will occur from time to time. It is called “Windows WMI Timeout” for the bakery. Not sure how it looks like in the .yml file exactly.
Ultimately this is an issue on the Windows side, and we will only be able to work around it to a certain degree.