Itunes has the function File>Add folder to library or File>Add file to library.
With these 2 functions you can add files again to the library even after you have renamed them to something better than the iTunes does.
So, unless you tell iTunes to delete tracks not only from the library but also from the filesystem, all your files should still be there.
If you need to cut the filename, then you may still use the Convert>Tag-Filename function, but you have to enclose the whole expression (e.g.
%discnumber%-$num(%track%,2) %artist%_ %album%
into the $left() statement:
$left(%discnumber%-$num(%track%,2) %artist%_ %album%,36)
cuts the filename to 36 characters.
Oh: if itunes is so picky about the filenames - why do you rename them anyway? Because if you rename them even with the preferred length but the filename is now different, then itunes will not find the files. The important bits should be the tags, the only thing a filename has to be is unique.