QGIS » QGIS Application

We have a number of shapefiles that have been created/edited in previous versions of QGIS where deleted features remained as phantom features (reportedly now fixed as per Issue 11007).

In the current LTR version (2.14.5) if these files are edited (feature deleted, split, merged or vertex added) then upon saving the edits, the entire file is corrupted - deleted features reappear, others disappear and attributes become completely reassigned to different features.
I have attached an example file that this occurs to.

I know this file suffers from the 'phantom' deleted features, because the feature count in the layers menu is higher than the feature count in the attribute table.
If a save-as of the file is done, the feature count of the new file matches that of the attribute table. This re-saved file can also have any edits done without resulting in corruption.

Not all files with these 'phantom' features behave this way - some can be edited and saving edits behaves exactly as expected, with the phantom features being cleaned out and all other data remaining as it should.

This file has had significant edits with large areas deleted, etc. so the resulting corruption is very obvious immediately.
Other files may be less obvious - how is a user to know when this will occur and ensure the file will not become corrupted after they save edits?

I had hoped that by making some edits that did not result in a change of object FID's (such as a simple attribute update) and saving those edits might result in a clean out ('packing') of the file, however this is not the case. It appears that perhaps the 'repack' function is only called upon saving edits such as deleting, merging or splitting features as well as adding a vertex to an existing feature. Even the addition of a new object does not seem to result in the cleanse of the layer :(