If VPOP3 receives the error message “-ERR Can't open the message file - it's gone!” from your ISP's POP3 server when it is downloading messages, this is a symptom of a fundamental bug in your ISP's POP3 server.
The error means that VPOP3 has asked for a message from the ISP's server, that the ISP's server had previously said was there, but the ISP's server is now saying that message has now gone.
The POP3 standard (RFC 1939) states, in section 4
Once the POP3 server has determined through the use of any authentication command that the client should be given access to the appropriate maildrop, the POP3 server then acquires an exclusive- access lock on the maildrop, as necessary to prevent messages from being modified or removed before the session enters the UPDATE state.
This means that once a POP3 client (eg VPOP3) has logged on successfully, the server (your ISP) should prevent any messages from being modified or deleted before the session ends (and enters the UPDATE state, after the QUIT command has been sent)
So, if a message has been deleted before the session ends, as the error message from the ISP is indicating, that is a breach of the POP3 standard. You should really take this up with the ISP's technical support because it is a case of non-compliance with the standards.
Further, it is not clear why the message has been deleted, so it may be that the ISP's POP3 server is randomly losing messages, or there may be mailbox corruption at the ISP and this may need urgent investigation by the ISP.
When VPOP3 receives this error from the ISP it will drop the connection and report an error to the administrator, because this is an unexpected event. VPOP3 will then reconnect at the next scheduled connection time and continue downloading messages.