The fresh search will come up with the same files because when the packages are rebuilt they still link with libstdc++.so.6. The way I did it was to save the list of files that were being rebuilt so that I could do the rebuilds in sections and remove the packages that were rebuilt.
Did you find a solution to this? I'm having the same problem (except with 542 packages that keep being rebuilt). I tried the emerge --resume --skipfirst as shown below but it didn't work:
emerge --resume --skipfirst
!!! Repository 'x-portage' is missing masters attribute in '/usr/local/portage/metadata/layout.conf'
!!! Set 'masters = gentoo' in this file for future compatibility
* IMPORTANT: 3 news items need reading for repository 'gentoo'.
* Use eselect news read to view new items.
* One or more packages are either masked or have missing dependencies:
*
* >=dev-libs/icu-4.8.1.1:0/58.1= pulled in by:
* (app-misc/tracker-1.8.0:0/100::gentoo, installed)
*
* >=app-text/poppler-0.16:0/65=[cairo,utils] pulled in by:
* (app-misc/tracker-1.8.0:0/100::gentoo, installed)
*
* >=media-libs/libass-0.9.10:0/5= pulled in by:
* (media-video/mplayer-1.3.0:0/0::gentoo, installed)
*
* The resume list contains packages that are either masked or have
* unsatisfied dependencies. Please restart/continue the operation
* manually, or use --skipfirst to skip the first package in the list and
* any other packages that may be masked or have missing dependencies.
ralph ~ # emerge --resume --skipfirst
!!! Repository 'x-portage' is missing masters attribute in '/usr/local/portage/metadata/layout.conf'
!!! Set 'masters = gentoo' in this file for future compatibility
* IMPORTANT: 3 news items need reading for repository 'gentoo'.
* Use eselect news read to view new items.
emerge: It seems we have nothing to resume...
I'm re-running revdep-rebuild now but it's starting all over again.