Custom keybind overwritten with a default setup by the patch as expected. Only changes I could see was some new keys to control the new GalNet audio playback. Was able to get my old custom binds back by copy pasting those new Galnet Audio keybinds to the end of my old V2.0 custom file and also change the major version number to "3" and also rename the file to include the 3 version to be safe.
So for info in case anyone else is wondering why their controls have been reset here is what I did to quickly get back what I had before:
1) Start the game and go into control settings, and see that your beloved finely tuned V2.0 custom key bind files has gone.
2) Force a new V3.0 custom keybind file to be created by picking a random control and setting a random key, doesn't matter which, just needs to create the new custom file.
3) Quit the game. Go to the keybinds folder which is in C:\Users\<yourname>\AppData\Frontier Developments\Options\Bindings. In there there should be the new Custom.3.0.binds file and your old custom.2.0.binds file, maybe with a .backup extension. Preferably you made a backup before to be sure, but it appeared to create one anyway and store it in this folder.
4) Open your old bindings file in a text editor and change the version number on the second line in the file from "2" to "3" where it says MajorVersion. Mine now says <Root PresetName="Custom" MajorVersion="3" MinorVersion="0"> Don't know if this is critical but I did it anyway.
5) Open the Custom.3.0.binds file in another window and scroll to the bottom. Copy all the GalnetAudio lines from this file to the end of your old custom file, making sure to insert it above the final </Root> line. Mine looks like this.
Code:
<GalnetAudio_SkipForward>
<Primary Device="{NoDevice}" Key="" />
<Secondary Device="{NoDevice}" Key="" />
</GalnetAudio_SkipForward>
<GalnetAudio_SkipBackward>
<Primary Device="{NoDevice}" Key="" />
<Secondary Device="{NoDevice}" Key="" />
</GalnetAudio_SkipBackward>
<GalnetAudio_ClearQueue>
<Primary Device="{NoDevice}" Key="" />
<Secondary Device="{NoDevice}" Key="" />
</GalnetAudio_ClearQueue>
</Root>
6) Save your new proper custom keybind and give it a new name. Not sure if it matters but I think it needs to end in ".3.0.binds", so mine is "MSFF2.3.0.binds". It should then in theory appear in the drop down keybind list next time your start the game.
Your mileage may vary but this worked for me.