This is nothing cryptomator can influence. Because cryptomator does not sync anything.
If you want to free up space by deleting offline files (without actually deleting the corresponding online files) you have 2 options
if supported by your cloud storage providers sync app, you can enable the files on demand function, which does exactly this. If you then tell the client to free up space, it will delete all local files that are not used at the moment. This will include the cryptomator vault files. If you try to access them again, the requested file will be downloaded.
do not sync your files (important, because if you do and delete your local files, then your online files will be deleted by the sync client as well) and access your files directly online. This is also possible for cryptomator vaults, but instead of the cryptomator App you have to use cyberduck (which has the cryptomator encryption technology included)