Ok I’m a little clearer on what you’re trying to do now 
Note that the label track and the labels are part of the Audacity project and are NOT part of a WAV file (In general WAV files do not carry metadata). In Export Multiple the labels are used to create the name of each WAV file.
I don’t’ use Audacity to remove clicks and pops - I prefer to use a piece of s/w called ClickRepair (it costs a little but is well worth the outlay IMHO). See this sticky thread: https://forum.audacityteam.org/t/click-pop-removal-clickrepair-software/1933/1
My outline workflow is:
- Record one side of an LP (aiming for a max level of c. -6.0 dB)
- I either mark the approximate track/song starts as I am recording by placing labels (CTRL+B will mark the current cursor position or CTRL+M will mark the current record/playback position). Or after the recording I zoom to fit the entire project and then I can usually visually spot the track/song start points and label them approximately.
- Export a single WAV file of the project
- Process the WAV file through ClickRepair
- Import the repaired WAV file back into the still open Audacity project
- Delete the originally recorded track in the project - this leaves the label track and the cleaned up audio (still in synch.)
- Edit the inter-track gaps: fade-out/proper silence/fade-in and possibly shorten the gap to clean off the LP surface noise
- Adjust labels to exact positioning
- Use the Amplify effect to bring the level up to -2.0 dB (0 dB can clip/distort in some players). I use Amplify versus Normalize as in Audacity Normalize works on each stereo channel separately and thus can alter/damage the stereo image.
- Export Multiple to create a set of WAV files (at 44.1kHz 16-bit PCM stereo)
- Exit Audacity
- Repeat for side-2 of the LP
- Back-up the set of WAV files (2 copies to 2 external USB disks)
Note that nowhere in this process do I bother to actually save an Audacity project. Also note that stages 2 and 3 give me temporary “backups” of the whole project that I can revert to if necessary. The only time I save the project is if I have to leave it part way through overnight.
WC