This is caused by Windows getting goofy with desktop high DPI scaling. If you run more than one monitor at different resolutions it will pop up from time to time, and isn't necessarily an issue with the game. There are a couple of ways to solve it, any one of the following should work:

1) Disable your second monitor before launching game (this normally gets windows to behave with DPI scaling)

2) After launching the offending app that jumps off screen, press Alt+Enter to try and force it back to fullscreen (rather than borderless windowed, which instead respects windows DPI)

3) Disable DPI Scaling for the offending app completely (for ES2, it's "C:\Steam\steamapps\common\Endless Space 2\EndlessSpace2.exe") by right clicking on the exe -> Properties -> Compatibility -> "disable display scaling on high DPI settings"

4) Turn off windows high DPI scaling altogether in the OS (not recommended if you run multiple displays with different resolutions, as it can give you headaches reading a 4k display with DPI scaling turned off. Use this option as a nuke-all last resort)

Delete the file in

My documents/endless space 2/users/<number>/Registry.xml

That will reset the resolution and should let you use it

Note borderless windowed mode is a tad fussy

Thank you, Satoru you fix worked, I didn't try any from Kornstalx but thank you all the same for the assistance have a great day.

Edited as Fixed and Closed