It looks like your annotations are in CriticMarkup format. Surprisingly I don’t see an Obsidian plugin that enables support for that. The equivalent in Obsidian would be ==Fiona==%%Gavin Blackwood’s mom%% (using Obsidian’s comment syntax) or ==Fiona==<!--Gavin Blackwood’s mom--> (using the more widely-compatible HTML comment syntax). It should be easy to search-replace You can use a fancy text editor like Visual Studio Code to search-replace across multiple files at once.
(If you’d like to see a list of your annotations, here is my slightly baroque method: List all highlights in document(s) — without community plugins!)
You might be able to use a file-splitting tool on Scrivener’s single-file export (after doing your search-replace on the single file to save up itself some work). Especially if you can find a Markdown-aware splitter and the files that were merged all start with a first level heading (# Like This).