Restart of the tomcat service did no good, unless I also restarted the Flash client. Then it was running without problems for a while, before it once again rocketed up to a 100% CPU load.
After some debugging we found the cause to be non-unique data rows to the SQLAssembler.
A database change led to a view was missing a join, which in turn caused the view to return a numerous duplicate rows. LCDS did not handle this very well, but was luckily easy to fix, once the bug was identified.
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