When converting to FLAC, it's always better to match the bitrate and format to the original files, if not there's a danger of losing some information, no matter how small, as a result.
Exactly.
That's why many softwares don't let you choose bitrate and format, but just keep the same ones when converting to flac.
Converting 16/44.1 wav to 16/44.1 flac doesn't make you lose anything.
Or 16/48 to 16/48, or 24/48 to 24/48 and so on.
The differences audible through the listening experience Chun is referring to, is real, but it is caused by the player.
Many players do not have the chance to reproduce the flacs, and others do but just converting on-the-go to wav, obtaining non-optimal results.
That's why for the listening (or editing) it is always advisable to use uncompressed formats as WAV or AIFF directly.
This doesn't mean that by converting WAV to FLAC or viceversa you get loss of data, but only that reproducing compressed formats (even if lossless) is not as good as reproducing uncompressed formats.
Lossless compression is useful for storage or sharing matters, and less for listening.
Even burning audio CD's (not data) using FLACs, makes your burning software to convert the FLACs to WAVs before burning.