I had the exact same problem. I solved it by:

- Deleting the container and image

- Create a task in task scheduler with root user and with the following config

docker run -d \
--name=calibre-web \
-e PUID=1026 \
-e PGID=100 \
-e TZ=Europe/Lisbon \
-e DOCKER_MODS=ghcr.io/linuxserver/mods:universal-calibre \
-e OAUTHLIB_RELAX_TOKEN_SCOPE=1 \
-e TP_THEME=aquamarine \
-p 8083:8083 \
-v /volume1/docker/calibre-web:/config \
-v /volume1/docker/calibre/BibliotecaCalibre:/books \
--restart unless-stopped \
lscr.io/linuxserver/calibre-web

Replace PUID and PGID by your own

It will this time install flask and all necessary python modules. All your data and configs will be preserved