Split off from another, non-technical thread:
I still play SP actively and running the dev exe resets my extensively customized settings in the normal game, very annoying.
That happens to me too and it is indeed very annoying, particularly that it resets the video resolution. Something the devs could easily fix... The rest [of the settings being reset] don't bother me as much. You can make a backup copy of your user.setting (or of the entire Settings folder to be sure) after using the regular exe and then just restore your backup after using the dev exe.
I do wonder if there ain't some bug there at work. Those files have internal format versions (of their own) so that when you upgrade Sins they can migrate settings as needed. But for the same version of Sins (1.82.5006), the production exe writes "Version 1241" to user.setting whereas the dev exe (of the same Sins version) writes "Version 241" (omitting indeed the first "1") to the same file. So when the normal exe then loads, it thinks it needs to reset/ignore the video settings and so forth. I'm not sure if this is by design (i.e. the first "1" in the user.setting version is supposed to indicate being written by the production exe) or if it is a bug that the dev exe writes a Version field that is 1000 less.