I've seen some posts on the clash that manifest itself when you have both FlexBuilder 2 and FDT installed. Both plugins want to claim the *.as ( Actionscript ) file type association for their editors which results in weird errors such as disappearing views, opening Actionscript 3 files with FDT (which does not support AS3 yet ).
The solution is quite simple: use different workspaces for your Flex projects versus your Actionscript 2 projects. You can then link the *.as file type association for AS3 files to FlexBuilder 2 in your Flex projects workspace and in your other workspace you link the *.as file type to FDT. Now till FDT doesn't support AS3 i'd say this is the easiest way to handle your projects. Darron has some more tips on different workspaces. Note that FDT 1.5 ( a free update that was released last week ) supports file association of as files via Content Types in Eclipse but i think seperating your projects between workspaces is a much better solution.