If, for example, you mark a test for REBASELINE in platform/chromium/TestExpectations, and there is an overriding line in the skia_test_expectations.txt file, webkit-patch rebaseline-expectations will not see the line with the REBASELINE.
After r127057, at least we'll log a warning that we didn't find a REBASELINE, but we should either be smarter about this (e.g., log a warning that tests are shadowing others) or stop using rebaseline-expectations altogether ;).
changing subject from
"expectation overrides can cause REBASELINE modifiers to be missed"
"rebaselining doesn't really work w/ multiple expectations files"
I don't expect to work on this in the webkit.org repo in the foreseeable future, so I'm clearing the 'assigned_to' field in case someone cares to take a look.