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Using export to save the sprite or tile sheets to an external file, and then import to load them back in, does not preserve the sprite flags. Looking at the emitted files it seems like they are just "plain" PNGs without any ancillary chunks.
This should probably be handled the same way as save png handles the embedded cartridge data: write an ancillary chunk (flAg, perhaps?) containing the 256 bytes of flag RAM corresponding to the exported sheet, and when importing, if that chunk is present, load it into flag RAM.