Yes, from recently, I'm like you, I have classes that are dealt ith by custom fileds and AngularJS, so I can't anymore use the cleaning feature.
I have a workaround though: anytime I create a useful class that is not going to be attached to an element in webflow, I document it in a page called Dashboard, and attach it to a square element. So it's used and I can clean without fear.
I use this Dashboard page to gather all my important Symbols that are sread on all the site, so when I have content update, I can do them easily on one page. Also, when I have an element set to opacity 0 for interactions, I try to make a symbol of its content, then put the symbol on the dashboard page, so I don't have to manipulate anything to edit the hidden content.
I also put styles with color reference so I can edit them all in one place for harmonization.
Hope it helps!