Muddy sound after reprocessing

I’m trying to remove a few clicks & than separate tracks on a 24/96 FLAC file that was recorded on a Linn LP12 turntable & Ittok arm using audacity. The original file sounds very open & precise but after removing just a few clicks & outputting to a 24/96 WAV file it’s slightly muddy & compressed. At this point I’ve done no processing other than use the Draw & Repair tools to remove 2 clicks, save the project and export to WAV. Any ideas why the sound quality is impacted? Any help would be greatly appreciated! Thanks

Do you still have the original file?

There’s no logical explanation for that… Audacity is “bit perfect”, except for some inaudible dither.

You can turn-off dither, and that would probably be the “best practice” since you don’t want to touch 99% of the file. But in practice it doesn’t matter. Dither is not audible at 16-bits, it’s even quieter at 24-bits, and way-way-way quieter than vinyl surface noise.

& outputting to a 24/96 WAV file

Are you listening on the using the same audio-player software as you were using for the FLAC? Have you re-listened to the FLAC to make sure nothing has changed in your setup?

The original file sounds very open & precise

What does THAT mean? Frequency response?

slightly muddy

Frequency response again? Loss of highs? Or some kind of distortion?

& compressed.

[u]Clipping[/u] is a (very-bad) kind of dynamic compression. That’s about the only way you can “accidently” get compression, but there’s no way that can happen unless you boost the volume.