Are you doing this:
1. Select WAV file
2. Select Convert Format...
3. Select FLAC Encoder
4. (skipped)
5. Click button Convert
If so, add a step:
1. Select WAV file
2. Select Convert Format... (usually available via right-click)
3. Select FLAC Encoder
4. Click Options > "Leave original file, add destination file to library"
5. Click button Convert
You'll end up with two files with the same name but different extensions/types, the original WAV, and a new FLAC. After you are comfortable that the FLAC and WAV are 100% identical lossless audio (as they should be), you can delete the WAV.
If this is how you want to handle most file Convert actions, just select the desired Options once; MC will remember. For future tracks, you'll find FLAC is already selected, and so are the Options, so you can just click button Convert.
This is how my MC is set (has been for years) because it is safe and quick. Converting WAV to FLAC is a one click action. It is possible to select a batch of WAV files, click once, and they will all be converted.
However, there are other ways to get to the same result in case other factors are involved.