Of course it will, because you just deleted part of the payload that is required by the bittorrent client.
in other words, utorrent stores the cross file pieces in the temp file and wont flush it out to the individual files
ALL bittorrent clients do, uTorrent uses a file called utPartFilexxx.dat qBT uses a folder called .unwanted
Windows explorer does not need or use the "unwanted" data because that 'belongs' to a file that isn't there.
From your other post, you seem to think that if you download the largest file then it may have all the crossfile pieces? but how do i force the client to force the pieces to files on disk !!!
That's not what I said, and it is nothing to do with what you download, but
how the torrent was created.
For the sake of this hypothetical scenario the payload has 15 files in a 692MiB payload, piece size 1MiB (692 pieces total)
In the default size order;
File 7 is 650MiB so occupies P0 to P649
File 4 is 10 MiB so is in P650 - P659
files 3,5,6 & 8 are 5.5MiB each so are in P660 to P681 (22 pieces)
file 1 is 1.5 MiB so needs 1.5 pieces P681 to P682
file 9 is 1.2 MiB so need the other half of plus a bit more, so P682 and P683
file 2 is 1.0 MiB so uses P683 and P684
the rest of the files range from 600kiB to 20kiB so are spread across P684 to P691 (I'll let you do the maths)
Now if you WANT file 9 but NOT file 2 P683 still has to be downloaded so HAS to be saved somewhere.to complete the binary structure. and if you re-arrange the files in name order and work out what pieces the occupy, you WILL see how the cross-file scenario gets MUCH worse.