This sounds a lot like what I'm getting as well. I'm using ES 7.0.1 and while I get data displayed in the Discover tab, that data is only for Filebeat versions 7+. My index that has Filebeat 6.7.1 data, however, returns nothing. Regardless of whether I'm looking at 7+ data or 6.7.1 I, too, get the 1 on x shards failed but all are green. I posted a question about this yesterday, but haven't gotten an answer. The question I posed is here.
Glad it's not just me!