I have a three part answer.
1. You should not use import ASCII to change an existing netlist. It only overwrites or adds data.
2. You can use Layout's ECO mode to add and/or delete connections on the PCB. This is a quick fix in your case.
3. There are two correct ways to make ECO changes from the schematic to the PCB, and back again.
The first is through OLE. Select Tools, then PADS Layout. This links the two databases for cross-probing, and also controls an interactive ECO process. The help files should guide you through the steps you need to make.
The second is my preferred method. Create the netlist as you did, then in Layout, click on Tools, Compare/ECO. This will bring up the Tools for complete control of making updates to the PCB. Again, use the Help tab to learn all of the options on all 3 tabs. I believe it's always advisable to review the changes being made, if only to verify they are indeed the ones you expected to make.
Thanks, David. That fixed it,
I guess I have to get the Protel paradigm completely out of my head.