So out of curiosity, I poked around at this. It seems the original wav in it's current form can be encoded to flac with no problem, but it doesn't decode properly. (I couldn't hear a difference, but I only have my phone to listen to it atm)
You need to use sndfile-convert to convert the wav to wavex.
I'm not sure if this step is lossy though.
$ sndfile-convert 'Underwater Explosion 01.wav' 'Underwater Explosion 01.wavex'
Then use flac with the --keep-foreign-metadata option when encoding the new wav file.
$ flac -sV8 --keep-foreign-metadata 'Underwater Explosion 01.wavex'
NOTE: --keep-foreign-metadata is a new feature; make sure to test the output file before deleting the original.
Then check it out with sndfile-info
$ sndfile-info 'Underwater Explosion 01.flac'
========================================
File : ue.flac
Length : 672669
FLAC Stream Metadata
Channels : 2
Sample rate : 96000
Frames : 405700
Bit width : 24
Seektable Metadata
Vorbis Comment Metadata
Application Metadata
Application Metadata
Application Metadata
Application Metadata
Application Metadata
Padding Metadata
End
----------------------------------------
Sample Rate : 96000
Frames : 405700
Channels : 2
Format : 0x00170003
Sections : 1
Seekable : TRUE
Duration : 00:00:04.226
Signal Max : 5.90136e+06 (-3.05 dB)
You must also use the --keep-foreign-metadata option when decoding the file.
$ flac -d --keep-foreign-metadata 'Underwater Explosion 01.flac'
The md5sums from the wavex and decoded flac match
$ md5sum *
6516d76e103f9357554c3620bbd9dcec Underwater Explosion 01.flac
39f1126a623a06f5d97b9ebbf6ad6a83 Underwater Explosion 01.wav
39f1126a623a06f5d97b9ebbf6ad6a83 Underwater Explosion 01.wavex.orig
9719cdf32d927ec4006f83dae165a030 Underwater Explosion 01.wav.orig