Can you please post your complete project so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
You have a little leftover from the changes you made.
Mark the shift register with left click.
Type ctl-x to cut it out. You will see the small green signal line.
Mark the line with left click and delete it.
Type ctl-v and place the shift register to its original place.
The design will not fit in to this device. I added signals to all the Shift Reg's and the fitter says you have max of 4 Data Paths and you need 7 Data paths. I would suggest you change your design to PSOC 5 device.
The reason why the square around the shift_out pin disappeared is there is a show wire connecting to the pin as follows.
You can select the wire by pressing your mouse at the upper-right place of the pin where no components/wire is existing and dragging to the lower-left place of the pin. Once the wire is selected, you can delete that wire.
The second and third shift registers were attempts at discovering the source of my stated problem... but thanks.
Bob and Noriaki.... many thanks. It must have happened in one of those rubberbanding scrambles.