Footprints get floated when running "Update PCB from Schematic"

Description

Footprints are floated when running "Update PCB from Schematic"

Steps to reproduce

1. Open kit-dev-coldfire demo and run Eeshema
2. Run "Update PCB from Schematic"

At this point, pcbnew opens and we expect that netnames change due to netlisting differences for automatic names. All footprints should remain in place. Instead, JP101 and U201 are floated as if they were new footprints in the schematic.

Note that this also happens to schematics when adding footprints to adjacent nets. It seems to depend on the netname.

KiCad Version

Application: KiCad
Version: (5.99.0-801-gceceb6c39), release build
Libraries:
    wxWidgets 3.0.4
    libcurl/7.64.0 OpenSSL/1.1.1d zlib/1.2.11 libidn2/2.0.5 libpsl/0.20.2 (+libidn2/2.0.5) libssh2/1.8.0 nghttp2/1.36.0 librtmp/2.3
Platform: Linux 4.19.0-6-amd64 x86_64, 64 bit, Little endian, wxGTK
Build Info:
    Build date: Jan 25 2020 07:42:18
    wxWidgets: 3.0.4 (wchar_t,wx containers,compatible with 2.8) GTK+ 3.24
    Boost: 1.67.0
    OpenCASCADE Community Edition: 6.9.1
    Curl: 7.64.0
    Compiler: GCC 8.3.0 with C++ ABI 1013

Build settings:
    KICAD_SCRIPTING=ON
    KICAD_SCRIPTING_MODULES=ON
    KICAD_SCRIPTING_PYTHON3=ON
    KICAD_SCRIPTING_WXPYTHON=ON
    KICAD_SCRIPTING_WXPYTHON_PHOENIX=ON
    KICAD_SCRIPTING_ACTION_MENU=ON
    BUILD_GITHUB_PLUGIN=ON
    KICAD_USE_OCE=ON
    KICAD_USE_OCC=OFF
    KICAD_SPICE=ON