S3D already has a profile system that makes it easy to store different printer settings, changes for different materials, and so on. That system is stored completely separately from the processes, so you could delete all of your processes and your machine/filament settings would still be there.
It sounds like you weren't using the profile system, and instead were storing all of your machine and filament settings each as a separate process. That's definitely not a good idea since many of the existing S3D tools will change and reconfigure your processes (those are intended to change for each print).
If you want to move your settings from a process to the profile database, just double-click on the process and choose Save As New.