I think you can make it through unless you just have a big valuation problem.The VA and lender might let these repair issues slide or you might have to agree to fix some things out of your own pocket if the seller refuses.Maybe the seller would do it or go 50/50? If I wanted the house I would fix things for which the cost didn’t substantially affect the deal,especially if I agreed to take the property “as is” previously.As a seller I have had people come back and ask for repairs after writing an “as is” offer. It really pissed me off but I met them something like half way.The seller probably realizes it is good for them to cooperate but if they can’t afford to, have doubts about selling, or back-up offers you lose leverage.

I think your agent is being realistic in telling you “there will be others” if this doesn’t pan out.She probably could have made a better evaluation earlier but nobody is perfect. In any case you should talk to your lender about these questions immediately.

Not all deals are going to make it. Hopefully your agent is taking good care of your concerns given the situation . Ask her if your earnest money deposit is being protected regardless of how this plays out.