You should only run into that problem if your compressor compresses in MANY one byte chunks, so basicly your compressor should never cause a problem.
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Terrain is first in the vgagr# files, then objects.
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On another note, I've decompressed and recompressed some of the Lemmings DATs, namely "main.dat" and "vgagr0.dat" and my compression method produces files that are a often few kB smaller than the Psynosis compression!
MAIN.DAT - 56,472 bytes
recompressed - 53,445 bytes
LEVEL000.DAT - 3,722 bytes
recompressed - 3,717 bytes
VGAGR0.DAT - 24,464 bytes
recompressed - 22,928 bytes
VGASPEC0.DAT - 28,655 bytes
recompressed - 28,146 bytes
ADLIB.DAT - 12,988 bytes
recompressed - 12,790 bytes