How about this as a solution…:

The edit entry dialog could have an option (checkbox) which would flag an entry as “not paid/pending”.  When this flag is set, we’d set some kind of indicator icon on the entry row (in the calendar) to visually show that the item is not paid.  Then to change this indicator, you can use the edit entry dialog to uncheck the value, or perhaps we can hook up the right mouse click to also do that as a shortcut.  Then, when the checkbox is not checked, the indicator will be removed and it will look like the rest of the entries.

This checkbox would default to unchecked so we don’t force people in to this scheme.

Bank import consolidation would automatically remove the flag when it detects that this particular entries has been paid. 

Regarding some entries on the same day with the same amount – yes that could be tricky.  I’ll have to add some exception cases for this and make the user choose which title is paid and which is not if one is paid and one is not.