Currently, there is no official method to disable automatic updates for WSL from the Microsoft Store without removing the Store's ability to update entirely. The abrupt shutdown of running WSL instances during updates has been noted by multiple users, and it appears to be a known issue. Unfortunately, as of now, there hasn't been a response or solution provided by Microsoft regarding this specific concern on the WSL GitHub repository.
For users looking for a workaround, the best practice would be to regularly save your work and close WSL instances before updates are likely to occur, although this does not prevent the issue from happening unexpectedly.
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