This is something that I have seen frequently as CLIP STUDIO PAINT gets more popular, yet little no answers are given on why sometimes it doesn’t save your settings when you reopen it. There are actually several things that can potentially prevent it from saving, but I will only talk about one because it is by far the most common.
CLIP STUDIO PAINT will NOT save your settings if you have closed it improperly/prematurely.
If you have closed CSP with task manager by ending its process, if it was closed when not responding instead of waiting, or if you shut down/restarted the computer before closing it first, CSP will not save any changes made to the program. This INCLUDES any modified, added, and deleted brushes/tools.
Can you get those settings back? Is there a file?
The short answer is no, the long answer is that there is no tmp file made to store those changes. No file means there is no way on getting those settings back. After the program closes properly though, all changes made to settings will be stored in your user documents, under directory CELSYS_EN/CLIPStudioPaintVer1_1_0 * or CELSYS_EN/CLIPStudioPaintVer1_5_0 *.
It’s also a good habit to save backups of the CELSYS_EN folder occasionally, if you have room of course. Sometimes updates can override your changes and replace them with the default. Also, backups to your documents can be found here as well in the CLIPStudioPaintData folder.
* The directories mentioned are for the ENGLISH VERSION ONLY. If you have Manga Studio 5 (I suggest updating it, look on their website on how to do that), the folder is user documents Smith Micro/Manga Studio5_0_0. The Japanese version saves it as CELSYS (without the _EN).