Thanks for the feedback.
There is a restart functionality use the --restart option (see gmvault sync -h for more info).
Also note that when you restart from scratch, if the email has already been downloaded and is identical then the download is not performed. So only scanning the mailbox is faster than having downloads.
Regarding the timeout, please send me the error message you had and if it is a bug I will fix it but note that sometimes Gmail cut the connection without any reasons. There is also a retry reconnect process (up to 4 times) if it is not a fatal error (cannot recover from them).