Q:

Unite mailboxes via ssh?

Mailboxes are plain text. As I understand, they have to be parsed and every mail begins with its header. I have multiple "mailbox synonyms", like "Gesendet", "Sent" and "Sent messages". Is the following safe? 
cat Mailbox1 >> Mailbox2
rm Mailbox1

Will they be read correct after this action?

A:

There are two different mailbox formats and you need to know which one is being used.
The older format is MBOX and is a single file for each folder (if using IMAP).
The newer format is MailDir. This is much more common and now used by the majority of mail servers (Microsoft Exchange and Lotus Notes excepted of course). This uses a more complex folder and file format. Though the structure is still easily understood.
In either case, whilst you can use file system tools to copy, you need to make sure that a mail server is not trying to update the files at the same time. So generally, it is only safe to do so when the mail server is not running.
In the specific case you mention. If the format is MBOX, the copy will be readable by an appropriate mail client. But you may have broken the mail server.

