Can you add the option to set the HANDBRAKE_VARIABLE on the unraid configuration page and pass it over to the build script? This would be useful so people can change the version number without you having to rebuild it.
I think im having this exact issue. After a few hours i run out of log and docker space causing all my dockers to disappear. Where exactly did you put these parameters? As a variable in the docker gui or in a file on the appdata folder?
Edit:
I found the extra parameter option on the unraid gui by toggling the advanced options.