
You are most likely
not storing application data to a persistent volume.
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docker run --rm -it -v $PWD:/volume1 -v data:/data rednoah/filebot:watcher /volume1/input --output /volume1/output
-v data:/data ... mount persistent named volume "data" available inside the container as
/data (from inside the container) so that the
filebot instance running inside the container can remember things. If something is wrong here, or deleted, then
filebot will not be able to remember things.

What bind mount paths are you using when launching the container?

What does the console output say when you run
filebot -script fn:configure to write the configuration file?
(EDIT: nevermind; we already figured out where preferences are stored; see below)
EDIT:
Those settings are probably written to
$HOME/.java/.userPrefs but since
$HOME is a variable that depends on what user you're running as, I have no idea where the data is actually stored and if it is indeed stored to
/data somewhere. I'll look into adding configuration to the container to make this more explicit.
e.g. if you configure
filebot like so:
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docker run --rm -it -v data:/data rednoah/filebot -script fn:configure --def osdbUser=USERNAME --def osdbPwd=PASSWORD
then those settings are stored to
/data/filebot/.java/.userPrefs so you just need to make sure you don't lose or delete that information and configure your docker instance accordingly. This should typically not be an issue since all examples ensure that
/data is mapped to a named volume and thus not lost on container shutdown.