If you delete a ArcGIS Server from a site that has 10.4.1 running and leave the config-Store and directories, can you create a site for 10.6.1 and point to that config-store and directories folders that your old 10.4.1 was pointing to?
No, the version of the config-store has to match the version of the software. It would likely put the software in "upgrade mode" where it would upgrade the config-store to the same version. I haven't tested that nor have heard of anyone trying it so that's just a guess.
Are you trying to retain all the services, folders and registered databases that you had added while you were at 10.4.1 to 10.6.1?
As Jon mentioned, it is not a recommended procedure to map the old config store or the directories from an old server to a new.
However, I found this while some while trying to create some disaster recovery steps. I have tried this out only with the services, output, input and cache.
However, I will like to emphasize on the fact that there is no such documented workflow that has been given out by Esri and if in case any issues occur (performance or otherwise) Esri will not be liable for them. I have faced issues with overwriting and deleting existing services after resourcing the upgraded server to old folders and had to end up going with the recommended steps provided with Esri.
Hence to conclude, I would not recommend going ahead with this process unless it is suggested by Esri.
Retrieving data ...