For example:

For several files in https://cs.chromium.org/chromium/src/third_party/WebKit/LayoutTests/external/wpt/html/syntax/parsing/, there are multiple tests with different query strings, for example:

  .../html5lib_template.html?run_type=write_single
  .../html5lib_template.html?run_type=write
  .../html5lib_template.html?run_type=uri

Based on the logic at https://chromium.googlesource.com/chromium/src/+/master/third_party/WebKit/Tools/Scripts/webkitpy/layout_tests/controllers/test_result_writer.py#150, we're expecting that there should be separate baselines for separate tests, e.g.:

  .../html5lib_template.html_run_type=write_single-expected.txt
  .../html5lib_template.html_run_type=write-expected.txt
  .../html5lib_template.html_run_type=uri-expected.txt

But instead there is only one file:

  .../html5lib_template-expected.txt

One possible relevant area of code that probably needs to be changed:
https://chromium.googlesource.com/chromium/src/+/master/third_party/WebKit/Tools/Scripts/webkitpy/layout_tests/port/base.py#534

When this is fixed, the importer code that cleans up orphaned baselines will also have to be updated:
https://chromium.googlesource.com/chromium/src/+/master/third_party/WebKit/Tools/Scripts/webkitpy/w3c/test_importer.py#324