Problem with repeatedly compiling files with partly the same content and EmbeddedEclipse

Hello,
 
I am writing a Java-application that iteratively poses requests on
eclipse. Because I need good performance, I use an
EmbeddedEclipse-object following the mapcolorour-example. I always
create a file which usually contains some predicates as the file(s)
before (and, of course, some different ones). Then I hand over the file
to the rpc function.
Eclipse sends warnings, that some relations habe been replaced by new
ones with the same signature, and after a few iterations,  I get a
"Throw"-Exception thrown by the rpc method.
Now my question: Can I somehow reset the EmbeddedEclipse-object?
According to the documentation destroying (in order to instanitate it
again) will not help, since then no more EmbeddedEclipse-object can be
instantiated.
 
Thanks in advance
 
Cornelius
 
-------------------------------------------------
 
Dipl. Math. Cornelius Hagen
 
Lehrstuhl für Angewandte Informatik in den Kultur, Geschichts- und
Geowissenschaften
 
Feldkirchenstr. 21
D-96045 Bamberg
 
Tel: + 951 / 863-2843
 
E-Mail: cornelius.hagen@wiai.uni-bamberg.de
Homepage: http://www.uni-bamberg.de/~ba7ag99/cornelius_hagen.htm