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 www.sumatrapdfreader.org/settings.html for more information about all the settings which are currently stored and scripts/gen_settingsstructs.py for what to change in order to add new settings.

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