The Mac stores your custom words in a text file, located in the ~/Library/Spelling subfolder, with a filename using the international language code associated with which language you were using when it was added. You will also find some other files in there that should be ignored. What you want looks just like the language code, for example: en_GB and no file extension.
Load that in a text editor such as TextEdit to see if your words are actually there. I suspect they are and they just aren’t highlighting properly in Scrivener. There are some known issues with spell check highlighting in the latest version. As noted there, you might have better results with the spell check dialogue instead of live highlighting.