If a profile's USE flag for, say, djvu, changes so that the flag is always overridden off, any packages that use the flag are remerged even if they had previously been emerged with the flag unset. This caused me many hours of time wastage recently when kdehiddenvisibility was overridden off - it had always been unset on my workstation, but I had no alternative to remerging large swathes of KDE anyway.
Portage knows zero about use flag semantics, and will remain so... Use flags changed -> --newuse will trigger it. *** This bug has been marked as a duplicate of 81405 ***