So turns out the inconsistent id issues on the series was why watch data were being stored differently depending on how you refreshed your library/series last. It was also the reason why series merging was flaky for non-VFS managed libraries, and part of the reason why the "Next Up" and "Continue Watching" sections on the dashboards were not functioning as expected for Shoko managed libraries.
To remedy the aftereffects I'll recommend updating and running a refresh/scan with "Add Missing Metadata" on all your Shoko managed libraries, waiting for them to complete, followed by running the new "Migrate Episode User Watch Data" scheduled task afterwards, as these steps should fix the watch data and series merging issues.
Changes since last release
Here are the main changes since the last stable release (4.1.0):
fix: Add catch in try get method:
- Don't throw in the try get method for retrieving the file id.
fix: Add episode user data migration task.
fix: Improve logic in the episode user data migration task.
For the full list of changes, please check out the complete changelog here on GitHub.