In light of the new OGL stuff
 

Is there any software that can help me translate my (Admittedly vast) data to something I can put into Obsidian.md? I'm worried that WotC will come for Realmworks.

Sure. Farlings Realm Works Export Formatter Tool is designed to prepare your data directly for Obsidian.md. Even includes plugin support.

Tool Link
Tutorial

Note: to get Markdown output you need to select an RWEXPORT file, not an RWOUTPUT file. This means doing a "Full Export" from Realm Works and you will find the file in your "Realm Works/Export" folder.

RW is a system agnostic tool - you put into it what you want. (Plus its on your computer - is WotC really going to show up at your door and tell you to unistall?)

Why would WotC care about RW? If they wanted that cancelled, I'm sure any program/system that stores [or could store] D&D data would be in the same situation. They aren't going to be shutting down MS Word even though I have heaps of D&D data stored/created with it.

No-one really knows what the 1.1 OGL will be, if it actually happens. There's too much debate about what it MIGHT effect, and whether any of the OGL/licencing is legal to restrict in the first place. I'm seeing a lot of panic with people worried that "X" is going to banned/cancelled/pulled/unavailable. Don't panic! This might be the end of WotC, but its not the end of D&D and all its material or related systems.

That said, if Obsidian works for you, maybe it's a better choice. RW certainly isn't going anywhere or getting updates.

Note that the Output Formatter tool can't transfer your purchased RW content, since that content will never appear in the RWexport file that is generated by the Realm Works export function.