DYF files deleted on publish...?

I save a DYN in a personal working folder.
When I open the package manager, and I add the file to a package, then publish online, the DYF files are removed from the original location.

I understand they went into the Revit package folder:

C:\Users\xxx\AppData\Roaming\Dynamo\Dynamo Revit

but how do we manage custom nodes? How do you revise them and publish them again?

@Giovanni_Succi What version of Dynamo are you in? The reason I ask is that we did make improvements to change this behavior after Dynamo Core 3.3.
Initially the intend was to have a smart workflow to help users, say if they just create DYF’s and Dynamo can be smarter and can correctly places them in the right package folder. But we understand that the deletion from the original location was not ideal. So, we made the improvement to change that behavior in Dynamo Core 3.3.

Thank you Chinthya, here it is: