How about modifying your query with, say, "Field Name" < -999 (or try '=' since that is what you want to delete, correct?), and test to see what selected features there are as a result, use Get Count...if a count returned is the entire feature class count, then you know the query didn't work.
Then you can use Delete Features to get rid of the features once the selected set meets your criteria.
if not Count < total count: print 'whoa, better stop here...tell someone something unexpected has occurred' else: arcpy.deleteFeatures(features)
When you Delete Features with a selected set on the layer, it should only delete selected - the remainder should be untouched.
Still, it is a good idea to make sure that you have a selection with a count - if there's no selected features, the tool politely deletes the entire dataset and generates 'empty output'...that's kind of alarming!
In short, see this pseudocode:if not Count < total count: print 'whoa, better stop here...tell someone something unexpected has occurred' else: arcpy.deleteFeatures(features)
Results may vary, so always check what's actually going on in your code! Not sure what you mean about having invalid geometry - do you have points in a layer as you initially stated?...or are you trying to access an intermediate layer which is not persisted? One more thing, not sure how your gp environment is set up, but you have to have the overwriteoutputs property on.
EDIT- So if it is the case you cannot access these 'invalid' features, then try Repair Geometry.
You can zip the toolbox in which the model resides...zip it with a few output shapefiles if you can. ...or if too big, zip separately and post, no need to post your entire output...just a sample.
I may not be able to pinpoint this today (as I explained I am not in the office), but I bet once you post your zip, there are ModelBuilder experts that can fix it for you quickly! I still suspect your iterator -- are you sure it is 'aware' of the FCtoFC part of the process??
(oops, I meant go to Windows Explorer, select and zip the toolbox [tbx extension], etc.)