Shrinking an index will not change its Lucene version - if the original index was Lucene 6 then the shrunken one will be too.
However, it is supposed to be possible to shrink indices of either version in Elasticsearch 6.x (and we have test cases that check that this does indeed work). Please could you share a lot more information about what you're doing? It would be good to see the commands you're running against Elasticsearch as well as the full stack trace of the exception you quoted, and any log messages from around the time of this problem as well.