Yeah if bitpay says to send say 0.002 bitcoins and bittrex fee was 0.001 bitcoins then I'd send 0.003 bitcoins.

I can tell you that I thought bittrex fee was still 0.0002 like it used to be so I sent some transactions of with only a 0.0002 fee added and they eventually showed up on my bitpay they just took longer.

I've spoken to Poloniex before through their help department to see what happened to funds. They've usually responded as there shouldn't be anything hanging out there for 2 weeks like that.