Good to hear..
perhaps you made a symlink in fop2 to panel , in that way, you are sharing the location between fop1 and fop2, and after the update several files where copied over?
If you want to replace /panel with /fop2 the best way is to use an apache alias, as described in the FAQ. That way you can update the fop1 framework without modifying the fop2 files, and every link to fop1 will open up fop2 instead.
Best regards,
