You've hit on the key operational problem: the pattern format. Yes, you can copy the exact pattern string, but you must place it in the `.run` file correctly. It needs to be the property's value, not the whole command flag.
For example, if you edited your local script to add `--detect.blackduck.signature.scanner.exclusion.patterns=**/target/**,**/node_modules/**`, your `.run` file would need a line like:
`detect.blackduck.signature.scanner.exclusion.patterns=**/target/**,**/node_modules/**`
The caveat is that you should verify the property list is still supported in the fresh CI image's version of the tool. I've seen property names change between minor releases, which is another reason that local edit is just a test bench. Always check the release notes for the version baked into your CI container.
Logs don't lie.