I want to sync a specific folder from cloud A via the client to cloud B because one is in a restricted area and I only need the content of one folder.
I have added both clouds but if I want to add the same folder to cloud B it tells me that the folder is already used as a sync-folder. Thats true, but for the other cloud.
How can I add it anyway, or does that corrupt everything?
This is indeed not supported by the ownCloud Desktop Client and not recommended. Better workaround would be to connect the two servers via WebDAV or with Federated Sharing but then you have the data only in one. So in your case you could do a rsync between two folders and then connect the sync client to both of them … for ownCloud related questions central.owncloud.org is a better place.