Prolly what yer gonna hafta do is programatically edit the registriy prior to opening SW.
Edit the key
HKEY_CURRENT_USER\Software\SolidWorks\SOLIDWORKS 2018\ExtReferences: SolidWorks Journal Folders. Have it point to some random location that has write access. Open SW, then change the key back to what it was. SW only reads the registry when opening, and (at least it used to) only writes to the registry during a successful shutdown (as anyone can tell you whose customized a toolbar and then crashed SW).
Any idea how to do that in C#? I'm not exactly sure how to change the registry, trying to figure it out right now.
In case anybody also needs to do this here's the code:
RegistryKey key = Registry.CurrentUser.OpenSubKey(@"Software\SolidWorks\SOLIDWORKS 2018\ExtReferences", true);
key.SetValue("SolidWorks Journal Folders", @"C:\Some other folder path");
I also found that if starting many instances of solidworks you need to offset the starts since the registry can only contain one value at a time so if you go to load a second before the registry changed again you will get the journal pop up again.