I didn't answer your question when you posted it before because I didn't know what the answer was.
Thinking about it now, I believe that you need to say YES, because you have paid for and submitted an application for leave to remain, and the details of that application are currently in their system.
The issue I see with saying NO is that if your previous visa has now expired, then you are only legal in the UK right now because you have a valid application pending in the system (your FLR(M) status has been extended via 3C Leave)
So, if you say NO, then how can you prove that you are legally in the UK right now and therefore that you are making a valid application for ILR? Because if you say you don't have an application pending, you will have to show you have a current, valid visa... but you don't, because I assume your visa expired in April.
Also, the biometrics offices are now open and they are contacting everyone by email in application date order, to let them know that they are either allowed make their biometrics appointment now, or that they are eligible to forego giving biometrics for their application and only need to upload a new photo.
Have you had an email from them yet regarding your FLR(M) biometrics? I believe they are working their way through the applications submitted in May at the moment. For info, someone else on the forum who applied for FLR(M) on 24th March was able to book their biometrics appointment a couple of weeks ago and are attending it today.