Of course a left over construction folder inside #WAW does absolutely nothing. Run with it or without it, makes no difference, how could it? Just delete it.
You have some sound issue, I thought you fixed it with the correct settings in CONF.ini. If its back, whatever causes it for you, it is not a left over zip.file.
BATEP03.ZIP did introduce a new soundset for #WAW. Actually it was the old CUP soundset and should be there. Variations on #WAW/Classes-Sound can easily be modified, as above, or directly because the prs and soundfiles remain uncompressed.
For the majority of B.A.T. flyers the existing #WAW2 sounds are fine, excellent in fact, since they deliver Tiger33 flybys in a 412 environment.
However, you now say it was all good until BATEP03 - Well that's fine, roll back to then, you can still have the rest of the expansion pack content.
If you wish to 'roll back' your sounds, start by deleting this folder: ...Il2/#WAW2/Classes-Sound and the rebuild Classes-Sound from BAT26, where it first appears, to BATEP01 and BATEP02. Just take the Classes- Sound from each, in number order, and put them back into #WAW2 to reach the point you had, regarding the sound in #WAW2, before you installed BATEP03.