That's because the MAS version is constrained by the App Sandbox. Thor is not allow to access the folder where the Chrome Apps located after you log out or reboot. I recommend you to use the version in the release pages:
https://github.com/gbammc/Thor/releases

Hope it helps and thanks for using Thor :)

Thanks for letting me know, @gbammc, I'll try that and will reopen this issue if I run into any problems. Thanks!

That's because the MAS version is constrained by the App Sandbox. Thor is not allow to access the folder where the Chrome Apps located after you log out or reboot. I recommend you to use the version in the release pages:
https://github.com/gbammc/Thor/releases

Hope it helps and thanks for using Thor :)

@gbammc Could the issue only be addressed by downloading and installing from the release page manually? I tried to install through brew also not work 😢

For everyone having this issue - moving the app to /Applications fixes the issue for me, the shortcuts no longer disappear.