This metric/warning should have no effect in indexing. The query_total is the number of shard _searches executed so far, and filter cache evictions counts the number of times something in the filter cache is removed/replaced because you have reached the limits - this is affected by filters in your queries. Filter cache evictions are normal as part of running your queries, although the filter cache size can be increased (or decreased) as needed. But before you do that, I'd probably find out first why search is slow by analyzing your queries.
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