I recently upgraded to 2017.1 from 2016.3.
After upgrading (update imported my settings from previous install), I removed the old 2016.x directory of the PHPStorm install.
When I went back into my IDE and opened a project, I noticed the Remote Host was showing "Could not connect to SFTP server at ...."
I opened the Deployment panel and saw that the username was missing. I re-input it, clicked OK, but as soon as the panel closed, the error came back under Remote Host. Opened Server panel again and the username was blank.
I opened several other Remote server panels (I have about a dozen different Servers), and all had the username blank.
I tried going into Settings|Deployment and entering it there, and clicking Apply, but the username value does not persist. Interestingly, all other values (host, port, root path, keyfile names, password) all seem to be there, but it will not keep username for some reason.
I've been upgrading PhpStorm for ~4 years the same way, the only thing I did different this time was delete the old 2016.x install directory after installation was complete, to clean things up (I have all the Jetbrains IDEs so my jetbrains directory starts getting cluttered after several upgrades).