Windchill will be running multiple queries during the remove action. Without profiling the action, it's hard to say exactly what query Windchill is running that's returning so many entries. But, you're getting the error because the number of entries returned by some query is higher than the value of your wt.pom.queryLimit property, which is apparently set to 100,000. If you increase the value of this property in db.properties, it should allow the remove action to succeed.
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