Update board from schematic issue when footprint pads have same pin number

Description

The attached minimal sample project shows an issue with footprint pads having the same number not properly updating the net due to what appears to be some internal pin numbering scheme. For some reason footprint "H2" in the provided sample shows all pads numbered "1" connected to net "unconnected-(H2-Pad1)_8" but the schematic net is "unconnected-(H2-Pad1)". It appears that somehow the original net for all pad number "1"s in "H2" were incorrectly set to "unconnected-(H2-Pad1)_8". When attempting to update the board from the schematic, the following unexpected update warning is displayed:

image.png

This is broken. The update should be replacing the "unconnected-(H2-Pad1)_8" net on the board with "unconnected-(H2-Pad1)" from the schematic.

minimal-update-from-sch-test.zip

This also affects the development branch.

Steps to reproduce

  1. Open the provide project.
  2. Open the board editor.
  3. Click the "Update board from schematic" button on the toolbar.
  4. Observe update results above.
  5. Click the update board button.
  6. Close the update dialog.
  7. Click on any pad "1" on footprint "H2" and observe the net has not changed from "unconnected-(H2-Pad1)_8" to "unconnected-(H2-Pad1)" as expected.

KiCad Version

Application: KiCad PCB Editor x86_64 on x86_64
Version: 9.0.6-rc2, debug build
Libraries:
    wxWidgets 3.2.8
    FreeType 2.13.3
    HarfBuzz 12.1.0
    FontConfig 2.15.0
    libcurl/8.16.0 OpenSSL/3.5.4 zlib/1.3.1 brotli/1.1.0 zstd/1.5.7 libidn2/2.3.8 libpsl/0.21.2 libssh2/1.11.1 nghttp2/1.64.0 ngtcp2/1.16.0 nghttp3/1.12.0 librtmp/2.3 OpenLDAP/2.6.10
Platform: Debian GNU/Linux forky/sid, 64 bit, Little endian, wxGTK, X11, gnome, x11
OpenGL: NVIDIA Corporation, NVIDIA GeForce RTX 3070 Ti/PCIe/SSE2, 4.6.0 NVIDIA 550.163.01
Build Info:
    Date: Oct 26 2025 14:39:40
    wxWidgets: 3.2.8 (wchar_t,wx containers) GTK+ 3.24
    Boost: 1.83.0
    OCC: 7.8.1
    Curl: 8.16.0
    ngspice: 45.2
    Compiler: GCC 15.2.0 with C++ ABI 1020
Build settings:
    KICAD_IPC_API=ON
    KICAD_STDLIB_DEBUG=OFF
    KICAD_STDLIB_LIGHT_DEBUG=OFF
    KICAD_SANITIZE_ADDRESS=OFF
    KICAD_SANITIZE_THREADS=OFF
Locale: 
    Lang: en_US
    Enc: UTF-8
    Num: 1,234.5
    Encoded кΩ丈: D0BACEA9E4B888 (sys), D0BACEA9E4B888 (utf8)
Edited by Wayne Stambaugh