Do you know what to do if an agent has your full manuscript but then you revise the entire thing and want to send them a new one but it's been 3 months?
This is not as uncommon as you probably think. Writers often revise their manuscripts during the querying process because it can take a very long time and feedback received during the process can lead to writers discovering the manuscript they thought was perfect when they sent it out, isn't quite as perfect as they thought.
Agents want to read your best work, so if you have significantly revised (not just corrected a few typos and changed a sentence or two around), find the email chain where they requested your full manuscript and reply to it with the new manuscript attached. The accompanying email should say something along the lines of:
"Dear Agent X,
Thank you once again for your request for the full manuscript of [Insert Awesome Novel Title]. Since this request, I have done a substantial revision on the manuscript and would prefer if you read this latest version.
Thanks so much,
Querying can take a long time, and some agents get very behind on reading requested material so there is the possibility that you'll get more feedback that resonates and you'll want to revise again before this agent gets to your work. If this happens, and the agent still has not responded, you can do the same thing again, but it is probably not the best way to give a great first impression.
Get your work thoroughly revised, beta-read and edited before you start querying. Then use the time while you're waiting to hear back to write another book, or some short stories to submit to publications that might raise your author platform. Resist the urge to keep tinkering with the novel you've just sent out unless you get feedback you just can't dismiss.