I was using CrashPlan too and I have converted my repositories to a common duplicacy storage.
To support different backup schedules, I do backup some folders in the user profile using an own snapshot-id, and so I have several snapshots per machine. All snapshots have some different filters and a common filter base set.
I use the preference
nobackup_file to exclude these folders in the backup of the user profile.
In my fork at github, I have extended the filter file syntax with a new statement to include another filter file.
@<filename>, you can now include other files. Relative paths are supported.
In addition I have changed the exclude behavior for the
.duplicacy folder. When using
nobackup_file, this folder will not get excluded anymore. I use filters that exclude cache and internal files (see this post).
I will make a pull request soon to include this feature