Persisted data is stored in SumatraPDF-settings.txt file. In portable version the file is stored in the same directory as SumatraPDF executable. In non-portable version, it's in
%LOCALAPPDATA%\SumatraPDF directory.
Starting with version 1.6 we also persist thumbnails for "Frequently read" list. They are stored in subdirectory
sumatrapdfcache as .png files.
See https://www.sumatrapdfreader.org/settings/settings.html for more information about all the settings which are currently stored and https://github.com/sumatrapdfreader/sumatrapdf/blob/master/do/gen_settings_structs.go for what to change in order to add new settings.