There was a startup in one of the YC W14 that had something similar to this case...

There was a startup in one of the YC W14 that had something similar to this case, but different scenario.

Camperoo, the technical founder quit, but she still moved on to apply to YC.

https://medium.com/@emmie/my-technical-co-founder-quit-the-d...

Perhaps you should still go ahead and apply!

But yeah like the jsprogrammer mentioned, add more details to here, there are lots of folks whom can give one or two words of advice. I've personally got some good feedback.