We seem to have come across an issue whereby a Shapefile that has been created/edited with previous versions of QGIS and has phantom (deleted) features, as discussed/resolved in Bug Report 11007, now edited in the current LTR (v2.14.5) becomes totally corrupted upon saving edits.
Upon saving, some of the deleted features reappear, others disappear and attributes become totally jumbled and attached to different objects in the table.
I have tried opening the layer, enabling editing, adding a feature and saving edits, removing the layer from the project and then re-adding, but this DOES NOT 'pack' the table and clean out the deleted features. Nothing I have tried except the trusty old 'save-as' of the entire layer, cleans it and reduces the feature count to the correct number of features. Without doing a save-as, if a new feature is deleted, or a node added to an existing feature (or an edit such as a cut or merge of features), then as soon as the edits are saved, a "_packed" version of the SHX and SHP is created and the shapefile that remains is corrupted.
Has anyone found a successful method to clean a shapefile without having to do a 'save-as' of every layer we have ever edited in QGIS?