If you’re going to use a lossless format, why not use one that is completely compatible with the DAW (number of channels, bit depth). WavPack is a better fit, spec-wise, with Nuendo than FLAC: I say keep FLAC, add WavPack.
My recordings and post-productions consist mostly of few tracks and are done on laptops: I could trade a few CPU cycles for less disc space.
Reaper, for example, has a very good lineup of writable file formats.
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Writable Formats: AIFF, APE, BWF, CD ISO (CUE/BIN), FLAC, MIDI, MOGG, MP3, OGG, W64, WAV, WAVPACK.
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Writable Bit Depths:
WAV/BWF/W64: 8/16/24 PCM, 32/64 FP, 2/4 ADPCM
AIFF: 8/16/24/32 PCM
WAVPACK: 16/24 PCM, 32 FP
FLAC, APE: 16/24 PCM