I configured an IMAP hotmail account in Thunderbird portable 45.3 as a backup.
I downloaded all emails and then I deleted the stored password (Options --> Security). Every time I open Thunderbird portable, it shows all email and tries to connect, but I don't enter the pasword to avoid synchronization. So this is working OK.
I made a copy in another drive. I opened Thunderbird portable and it showed all email and tried to connect and I didn't enter the password, but when I opened again all the mbox files from \Thunderbird45.3\Data\profile\ImapMail\imap-mail.outlook.com were deleted. I made a new copy to another drive and I got the same behavior.
The problem is related to moving Thunderbird portable to another drive or folder.
I made a test with Thunderbird Portable 52.1 and I got the same behaviour
What could be happening?