Emulator

Probable cause found by troubleshooting technique of replacing Global Settings from Portable one by one. No crash after replacing GCPadNew.ini

GCPadNew.ini is empty in Global Settings, while it is populated in the fresh Portable Mode Settings in 5.0-7232

Contents:
[GCPad1] Device = DInput/0/Keyboard Mouse Buttons/A = X Buttons/B = Z Buttons/X = C Buttons/Y = S Buttons/Z = D Buttons/Start = !LMENU & RETURN Main Stick/Up = UP Main Stick/Down = DOWN Main Stick/Left = LEFT Main Stick/Right = RIGHT Main Stick/Modifier = LSHIFT Main Stick/Modifier/Range = 50.000000000000000 C-Stick/Up = I C-Stick/Down = K C-Stick/Left = J C-Stick/Right = L C-Stick/Modifier = LCONTROL C-Stick/Modifier/Range = 50.000000000000000 Triggers/L = Q Triggers/R = W D-Pad/Up = T D-Pad/Down = G D-Pad/Left = F D-Pad/Right = H

** Additional Info **

The newer versions try to respect older settings, while adding new things, devs should rethink if it's worth fixing such conflicts one by one, or create some kind of different system, one of them is a conversion/normalization process where an internal utility would analyze the whole existing config and apply it over the newer defaults.

A new button would be added to Tools Menu "Rebuild Settings ..." with maybe some config before running the process, possibly selecting between global or portable config, etc.

1. First, the existing config would be backed up into a temporary zip file, excluding shaders, custom textures, larger files over X size, actually there could be a listbox with checkboxes with some of them checked by default and larger stuff unchecked but up to the user to decide.
2. Then the current dolphin version would delete the existing settings store(complete clean first), then write fresh default configs, after that is done it would reapplying the saved configs in the ZIP ontop, with some kind of smart merging algorightm that discards invalid parameters and/or values.
3. After that a new window would open with a report showing what was changed, plus generating a raw diff file possibly.

Now it may not be 100% but this system should easily fix such an empty file case, where it doesn't have to do any kind of parameter merging, just writing a new GCPadNew.ini file.
Most likely how to merge would have to be implemented manually per parameter, it won't just know all by it self, but the inital implementation of this feature doesn't necessairly have to be that advanced/complex, improved with time.

Auto Prompt For Settings After Crash - Currently I didn't found out any automatic logs being generated in the dev released version with or withoud debug mode (I can't build/debug in VS2017 right now due to an unrelated issue)
First some kind of record has to be created that dolphin has crashed (yes there's windows events but that's not cross platform)
Then maybe some conditions, for example, it has to crash X amount of times while doing this or that.
And a prompt would come up saying that it has detected crashes and asks the user to try Rebuild Settings or not, explaining what the utility does.

Sorry for grammar, I literally thought of this a minute ago and wrote it quickly.

Additional Info

Also all the missing parameter entries of various options would need to be figured out, some options don't have their INI entries written by default until the user enables/modifies them through the program GUI, personally I'm heavily not a fan of that.
All the settings that can ever be in the INIs and are not treated as volatile(current program-session only) and are meant to be savable, to have it's parameter entry written out in the settings files from the very beginning when the program doesn't detect any existing settings, the value would simply be the same as it is in the internal defaults, or no value at all even if that's okay (seen it before), that would make things easier in the merging/resolving process, but is also more clear when doing manual troubleshooting.

Also one other option in the Rebuild Settings ... internal utility would be to simply clear them without reapplying the old ones ontop - kind of a shortcut of doing it manually, that would be useful for the general public, not that I'm that lazy heh.

In the future, I would appreciate if you just report an issue instead of first reporting an issue and then coming up with nonsensical ideas that you think would solve it. This issue just needs a normal bug fix.