Apps keep disappearing

[stephen]

One thing comes to mind - See the post here:

Loosing layout after restart (Yosemite)

I use to have this problem, but after upgrading to Yosemite and changing how my monitors are connected, it’s keeping my configuration. One question, when I was having this problem, the computer would boot to my left-hand monitor, it would show the boot screen with the spinning wheel, now the progress bar. While in the display preferences under Arrangements the titlebar was on my right-hand monitor. Now it working and both the boot monitor and the titlebar monitor are the right hand monitor. So …

I’m wondering if this same issue is causing you to lose your apps in the OSX apps prefs.