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@Linwe,
When you say update, do you mean calibre update or FFDL update?
What is your OS type and version? Are you using 32 or 64bit calibre? Are you doing anything atypical, like a USB stick install?
FFDL keeps personal.ini and all it's settings in the calibre database for each library. Many other plugins store their config the same way. You should not need to re-enter them after updates.
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