this problem also occurs in both IDEA 4.5.4 and also in #3290:
I have an ant target that generates a lot of java sources.
the ant target starts java to do that, like this:
dir="$/source/resources" jar="$/source/external/wc/lib/wc.jar" fork="true">
<arg line="-java $/source/generated/java/src basetypes"/>
After that generation, at some point IDEA notices the modified sources and a popup appears that the new sources are read.
Afterwards if I hit ctrl-f9 I get "cannot resolve symbol ..." for each and every class that is certainly well within the project sources.
a full rebuild project is possible, but not rebuilding
just modified files with ctrl-f9.
Situation is resolved if I delete all system/cache, system/compiler
Seems like some problem in some cache to me,
and it is really annoying - sorry.