Hi.
I have managed to find a hand-written copy of pin-definition so that I can continue with the development of the project.
However, this should not have happened.
In my experience, an application, typically, would make a copy of your file before installing the default settings.
It is the normal and expected behavior. When you update a library, all the files of the previous version of the library are removed/replaced. If you have made any modifications to the library, they will be lost.
So you need to be prepared to port your modifications to each new version of the library following the update.
The IDE has no way to know this was "your file". It is just an arbitrary file in a library. The library author decided to set up this system where the user modifies the library code, but the IDE doesn't know anything about that system because it is not anything standardized. The library author should have clearly documented the need to back up this file to a safe location.
It is quite rare for it to be required for the user to make changes to the library code in order to configure it it. Most often, the library's API would be designed so that that the user can make any necessary configuration in the sketch code.