ChewyWeAreNotHome: Not sure if the issue is GOG deleting the file or if Hello Games is doing this. I plan to submit a ticket to both but first have to research which file contains the key bindings.
I happened to me with the first two updates and I have yet to install this one as basketball takes priority this time of year.
(Copied into this topic for continuity).
Also recall that resetting of key bindings was a problem in in many of the early updates in 2016 and/or 2017.
The file is C:\Program Files (x86)\GOG Galaxy\Games\No Man's Sky\Binaries\SETTINGS\TKGAMESETTINGS.MXML
By default, it's nearly empty. AIUI, only customized changes to the mappings are written to it. It's XML so a text editor which understands the grammar is helpful. Notepad++ if you don't already have a favorite.
I have (finally; I'm a slow learner ;-) made a backup copy in that same directory so I can quickly overwrite the default with my preferred keybindings.
One other note. The X key is interpreted in the game's remapper as "delete", so it's not possible to set it interactively. I map it to ; (Semicolon) and do a search/replace to change it to KeyX in the XML file.
FWIW, most of my customizations are driven by changing WASD style (pure evil) to ASDX (songs of angels) by rotating W -> S -> X -> W, and then a few more tweaks (G <-> Z, and so on).