We just upgraded to 9.9.5 and after the upgrade logged in to client no jobs are displayed. It says now that we have zero jobs and looks like a fresh install. Is this a known issue? What is the best way of going about restoring our software?

Didn't hear back from support but was able to import backup settings and reconfigure to get back up and running. Warning to those upgrading, backup your files because this update wiped everything out for us.

same thing for us
i noticed they changed the settings file names, the upgrade is buggy the first upgrade i lost all jobs, the second server i lost all ftp/sql connections

We just upgraded to 9.9.5 and after the upgrade logged in to client no jobs are displayed. It says now that we have zero jobs and looks like a fresh install. Is this a known issue? What is the best way of going about restoring our software?

Please upgrade to our latest version 9.9.6 and enable Extended server debugging before upgrading (and make sure its enabled after you upgrade still). You should be able to import backups from your backup folder in the Installation path.

We've had a couple of customers experience this, and 9.9.6 should fix this, but if for some case you experience this again, we have added a bunch of debugging information that makes it easier for us to track this down.

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