This is what worked for me: -
When you create a collection, add a data source, and refresh for the first time, the assets are added to the collection as expected. If you then delete the data source and add another one of similar type (explained below) the collection will still think it's looking at the deleted data source and not refresh the new one.
In my scenario I deleted a SQL Azure Database source and replaced it with an 'Azure Multiple' source. I think what is happening is, because the Azure Multiple source contains the same database that the database source did, the data wasn't getting updated as the metadata was somehow getting corrupt i.e. the collection still thinks the deleted source was there because it contained the same database.
To fix this, go to any asset in the corrupt collection and delete the data source at the top of the hierarchy (right hand side of the screen), this will remove all the assets from the collection and on the next refresh the collection will be updated from the new data source(s).
Note: Insights feeds from collection data, so if the collections are not up to date, then insights won't be either.