ECO has a number of choices, and it is not clear at first glance how they differ.
Netlist export is ADDITIVE, it will never delete anything, and will generate 'mixing nets' error
messages, if there are conflicts. So you get warnings, but no database fix.
ECO connect is a 'bigger hammer', it WILL syncronise the designs, and if that means
DELETE of parts, or connections, then it will do that.
There are a couple of choices to get it to 'do what you want'
a) Add the parts into the SCH, often down one corner.
Things like mounting holes can be a useful BOM tag, for a Case, for example.
b) Make the part non-eco registered. Under File.Library.Parts, untick [ECO Registered Part]
Another option is to edit the .ECO file before you import it into PADS.
You will see an entry like this:
Delete these entries and then your holes will not be deleted when you import the .ECO file.