Neither of these issues are anything to do with the new 3.9 release.
The Download All function is used by many people and isn't going anywhere.
The presence of those charts in the list for EDAB is a bug. It's related to the way we categorise AIP documents into instrument approach charts, visual approach charts and others. We do this with pattern matching and a recent inclusion of many more AIP documents resulted in some which are only relevant to IFR users being categorised as generic charts, which are visible to people who have IFR stuff turned off. Thank you for bringing this to our attention. Tonight these documents should be recategorised, though the change may take 24h to take effect.