Ah, so it doesn't seem specific to dgVoodoo's config. I had also noticed custom resolutions are being cleared in Radeon Settings whenever the second monitor is unplugged. The error I saw maybe suggests a problem with all resolution queries and possibly not only dgVoodoo.
See below for error details
[11512] [dgVoodoo] INFO: Available DirectDraw devices:
[11512] [dgVoodoo] INFO: Device 0: Name: "AMD Radeon R9 290X Series", Description: "\\.\DISPLAY19", Monitor rect: (0, 0, 1920, 1080), GUID = {67685559-3106-11d0-b971-00aa00342f9f}, system primary monitor
[11512] [dgVoodoo] INFO: DirectDrawEnumerateExA: Enumerating output devices.
[11512] [dgVoodoo] INFO: DirectDrawEnumerateExA: Primary device is enumerated with NULL GUID.
[11512] DirectDrawCreate (lpGuid = 00000000, lplpDD = 0019FA54, pUnkOuter = 00000000)
[11512] DirectDraw::Initialize (this = 049060C0, lpGUID = 00000000)
[11512] [dgVoodoo] ERROR: DDBase (00A00908): Cannot query supported resolutions on display output 0, list is empty.
[11512] [dgVoodoo] ERROR: DirectDraw (049060C0) Initializing failed: Cannot query supported resolutions on output device 0.
[11512] [dgVoodoo] ERROR: DirectDrawCreate/DirectDrawCreateEx: creating DirectDraw object has failed.
[11512] [dgVoodoo] INFO: DirectDrawEnumerateExA: Device 0 is enumerated to the application.
[11512] DirectDrawCreate (lpGuid = 6C0A4828, lplpDD = 0019FA54, pUnkOuter = 00000000)
[11512] DirectDraw::Initialize (this = 026F4008, lpGUID = 6C0A4828)
[11512] [dgVoodoo] INFO: Reading config from file S:\SteamLibrary\steamapps\common\Gorky 17\dgVoodoo.conf.
[11512] [dgVoodoo] INFO: INI file based version of config file is successfully read.
[11512] [dgVoodoo] ERROR: DDBase (00A00988): Cannot query supported resolutions on display output 0, list is empty.
[11512] [dgVoodoo] ERROR: DirectDraw (026F4008) Initializing failed: Cannot query supported resolutions on output device 0.
[11512] [dgVoodoo] ERROR: DirectDrawCreate/DirectDrawCreateEx: creating DirectDraw object has failed.
[11512] [dgVoodoo] INFO: Reading config from file S:\SteamLibrary\steamapps\common\Gorky 17\dgVoodoo.conf.
[11512] [dgVoodoo] INFO: INI file based version of config file is successfully read.
[11512] DirectDrawCreate (lpGuid = 00000000, lplpDD = 0019FE18, pUnkOuter = 00000000)
[11512] DirectDraw::Initialize (this = 026F4008, lpGUID = 00000000)
[11512] [dgVoodoo] INFO: Reading config from file S:\SteamLibrary\steamapps\common\Gorky 17\dgVoodoo.conf.
[11512] [dgVoodoo] INFO: INI file based version of config file is successfully read.
[11512] [dgVoodoo] ERROR: DDBase (00A00868): Cannot query supported resolutions on display output 0, list is empty.
[11512] [dgVoodoo] ERROR: DirectDraw (026F4008) Initializing failed: Cannot query supported resolutions on output device 0.
[11512] [dgVoodoo] ERROR: DirectDrawCreate/DirectDrawCreateEx: creating DirectDraw object has failed.
Thanks for taking the time to look at this. I enjoy your program.
Edit: Switching from DVI-D to HDMI fixed whatever the issue was with my single monitor set up. I don't think I understand enough about it to know why that's the case... Anyways, thanks again for your help!