After switching to ArcMap 10.2 I've noticed that my definiton queries will seemingly randomly remove themselves. I have no idea what triggers the deletion since I have noticed it after reordering items in the TOC, turning layers on or off, adding new layers, changing the symbology, even after Applying a DQ and having it show up then hitting OK only to have it not work.
I have tested the issue with a variety of MXDs, different project files, GDBs, SHPS, different company servers, etc. The issue arises for all of them. Recently, we completely removed all things Arc and are currently reinstalling things one at a time. We thought maybe it was one of the third party extensions that I use and have narrowed it down to either the DWR addons for IWFM tools or AquaVeo's ArcHydro extension. Things were going fine for a couple weeks after adding ArcHydro, and we thought the issue was maybe a caching or temporary file thing until yesterday when the problem popped up again.
I was just curious if anyone else has run into this issue, what things were tried on your end, and if you managed to fix it without having to call ESRI (I am NOT looking forward to calling ESRI, but that's the next step in this process since we cannot pinpoint it to a specific third party extension).