Before I came across the Applications folder (is it called that?) I found aseprite_auto_file and aseprite-extension_auto_file in HKEY_CURRENT_USER\Software\Classes\. Both of their shell\open\command keys were still set to an old path, I changed them, and it worked.
With the information that this could be stored in multiple locations, I have quickly compiled a full tree of any Aseprite related entries in the registry editor I came across:
.
├── HKEY_CLASSES_ROOT/
│ ├── .ase
│ ├── .aseprite
│ ├── aseprite_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command
│ ├── AsepriteExtension/
│ │ ├── DefaultIcon
│ │ └── shell/
│ │ └── open/
│ │ ├── command
│ │ └── ddeexec/
│ │ ├── application
│ │ └── topic
│ ├── aseprite-extension_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command
│ └── AsepriteFile/
│ └── DefaultIcon/
│ └── shell/
│ └── open/
│ ├── command
│ └── ddeexec/
│ ├── application
│ └── topic
├── HKEY_CURRENT_USER/
│ └── Software/
│ └── Classes/
│ ├── Applications/
│ │ └── Aseprite.exe/
│ │ └── shell/
│ │ └── open/
│ │ └── command
│ ├── aseprite_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command
│ └── aseprite-extension_auto_file/
│ └── shell/
│ └── open/
│ └── command
└── HKEY_LOCAL_MACHINE/
└── SOFTWARE/
└── Aseprite
And here is the same one, with comments for what I found there, what I did with it, and what seems to be needed for it to work.
.
├── HKEY_CLASSES_ROOT/
│ ├── .ase # Points to "AsepriteFile"
│ ├── .aseprite # Points to "AsepriteFile"
│ ├── aseprite_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command # Pointed to Steam- /
│ │ ├── # installed version on C drive (long gone),
│ │ ├── # changed it to D. Did not work, until the
│ │ └── # comparable item in HKEY_CURRENT_USER matched
│ ├── AsepriteExtension # Does not exist Aseprite wasn't installed via installer/
│ │ ├── DefaultIcon
│ │ └── shell/
│ │ └── open/
│ │ ├── command # Pointed to Aseprite from installer
│ │ └── ddeexec/
│ │ ├── application
│ │ └── topic
│ ├── aseprite-extension_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command # Pointed to Steam- /
│ │ ├── # installed version on C drive (long gone),
│ │ ├── # changed it to D. Did not work, until the
│ │ └── # comparable item in HKEY_CURRENT_USER matched
│ └── AsepriteFile # Does not exist when the installer version isn't installed/
│ └── DefaultIcon/
│ └── shell/
│ └── open/
│ ├── command # Pointed to Aseprite from installer
│ └── ddeexec/
│ ├── application
│ └── topic
├── HKEY_CURRENT_USER/
│ └── Software/
│ └── Classes/
│ ├── Applications/
│ │ └── Aseprite.exe/
│ │ └── shell/
│ │ └── open/
│ │ └── command # Points to Steam- /
│ │ ├── # installed version on C drive (long gone),
│ │ ├── # I did not change it, and it doesn't
│ │ └── # seeem to matter either
│ ├── aseprite_auto_file/
│ │ └── shell/
│ │ └── open/
│ │ └── command # Pointed to Steam- /
│ │ ├── # installed version on C drive (long gone),
│ │ ├── # changed it to D. Has to match the comparable
│ │ └── # item in HKEY_CLASSES_ROOT
│ └── aseprite-extension_auto_file/
│ └── shell/
│ └── open/
│ └── command # Pointed to Steam- /
│ ├── # installed version on C drive (long gone),
│ ├── # changed it to D. Has to match the comparable
│ └── # item in HKEY_CLASS_ROOT
└── HKEY_LOCAL_MACHINE/
└── SOFTWARE/
└── Aseprite # Came across this entry only when explicitly/
├── # searching for Aseprite releated entries, it has gone
├── # once I uninstalled Aseprite that was installed
└── # by installer