If I delete the manual and older version of plugin, I may be lost my progress more far. But if I keep both, the store plugin will be error.
For the next update, there should be update for plugin store. That's not enough if it just looks at the store only, but it should be made for all of plugins for all of manual-download and store-download plugins. So, there should be any conflict. Another feature can be a debug mode for plugin store.
I have an old trauma about replacing the plugins. But, try to imitating "Natural Pack Full ver." plugins which has combination of "Rural Plugin", " Natural Pack Demo ver.", and another new plugins.
IDK if my suggestion can be harmful, but I need that to manage the plugins.
In the image, I have a conflict with Cesare's Rural Plugin, I have both versions (first ver. from forum and second ver. from store). Few plugins have conflict too... 
Sorry for my bad English.
