You can increase the limit with a call like this when your application starts:
BooleanQuery.setMaxClauseCount( 10000 ).
That being said, using a huge number of clauses in a query will not perform very well. I’d recommend looking for another approach, for example filtering on a field that has the same value for all the documents you’re attempting to fetch. But without information about what you’re trying to do, I cannot really offer relevant advice.