Here's some steps to convert from ID3v2 to APEv2:
First, rename all of your mp3's that have ID3v2 tags (must have id3v2.dll installed) to a filename that contains all the data you want transfered:
%artist% - %album% - $num(%tracknumber%,2) - %title%
thats what i use.
Then use the masstagger to remove all tags. Remember if you have other tags you use put them in the filename too (or they will be lost).
Then set foobar to write tags in APEv2 format.
Now, masstag "guess tags from filename" using a matching string as the one you wrote from:
%artist% - %album% - %tracknumber% - %title%
ta-da you have APEv2-only tagged files. Enjoy.