To avoid this issue with TLH, I just use the latest version of FLAC Frontend and it FLACs them everytime
Sometimes when I have WAVs that are almost 4gb big[24/96 at ALMOST 2 hours], I get a WAV around 3.5+gb! Well, TLH ALWAYS chokes on them for some reason, but Ive ALWAYS had success with Flac Frontend! And even if you have WAVs OVER 4gb, there's an option to FLAC that as well! I ALWAYS save a RAW/MASTER WAV file, and then FLAC it so I can easily burn to a DVDR!
So if you have the ability to use Flac Frontend, Id give it a shot! Ive been using FF for well over a decade and its always been the most reliable FLAC'ing program for ME! I do use TLH for EVERYTHING else, but for FLAC'ing my 24/96 masters, I always use FF by default! As always, YMMV