Does FlexNet Connect support any authentication methods and how we can tell FlexNet Connect to use certain usernames and passwords?

Yes

Summary

This article will explain how to pass a username and password to a FTP/FTPS or HTTP/HTTPS in the download URL for an update in the FlexNet Connect Publisher site.

Question

Answer

FlexNet Connect supports HTTP/HTTPS and FTP/FTPS for the download URL and a username/password can be added by using the following syntax:

FTP/FTPS:

ftp(s)://<username>:<password>@server/setup.exe

HTTP/HTTPS:

http(s)://username:password@server/setup.exe