In this case, analyzers have strange encoding support and it has been deprecated in lucene.
For example someone using CP1251 in the russian analyzer is simply storing Ж as 0xC6, its being represented as Æ
LUCENE-1793: Deprecate the custom encoding support in the Greek and Russian
Analyzers. If you need to index text in these encodings, please use Java's
character set conversion facilities (InputStreamReader, etc) during I/O,
so that Lucene can analyze this text as Unicode instead.
I noticed in solr, the factories for these tokenstreams allow these configuration options, which are deprecated in 2.9 to be removed in 3.0
Let me know the policy (how do you deprecate a config option in solr exactly, log a warning, etc?) and I'd be happy to create a patch.