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The current code ignores the FILLS section in DEF as seen at https://github.com/KLayout/klayout/blob/master/src/plugins/streamers/lefdef/db_plugin/dbDEFImporter.cc#L1420.
I've had to resort to re-parsing the DEF in python to create the fills. Please support FILLS as they are a necessary part of DEF to get a correct GDS out.