Using Spek to see if an audio file is really lossless after doing noise reduction.

I digitized several vinyl LP’s and couldn’t figure out why some FLAC files do not pass the Spek test for lossless. Then I saw that if I do noise reduction based on the vinyl noise between tracks, the Khz of the whole file drops and it looks like it’s not lossless anymore. Do I have to stop getting rid of vinyl noise to have a lossless file? The file sounds cleaner with the noise out but then it looks like an MP3 on Spek!