My knowledge of fiberglass sandwich constructions is limited. There is some good literature on composite materials and their use in marine / recreational applications. They are available in form of many pdf’s and written in an understandable way. I will try to locate them and post a link.
Contrary to a previous post I belief that the core (foam, balsa, hex cell,…) in a well constructed sandwich construction is an essential part of this construction that provides strength and weight reduction. If it would be solely the basis to place layers of composite material (fiberglass, Kevlar, or carbon fiber) separation issues like with Hobie hulls would not result in soft spots. (Jim IIRC you build rudder blades as a sandwich construction – I might confuse you with some one else)
From what I have learned in the past and from pictures I have seen the more common failure among Hobie hulls seems to be the separation between foam core and the inner and outer hull shell. According to what I have seen so far the individual layers of fiberglass are less likely to separate (delaminate). Here in TX al lot of older (pre 80’s) Hobie’s have this issue. Some people claim that this type of separation between hull composite material and foam core might be due to high outside temperatures, water that remained in the hull for extended periods of time, pressure / loads put on areas of the hull which compressed the foam core to much, …
Fscot… I think your approaches to the issue are pretty good. I never liked the idea of filling the voids between foam core and fiberglass shell with epoxy (weight issues – especially when the separation extends over half of the deck. Removing and replacing the core is a good idea
The “drilling out” method…it might be difficult to monitor if you removed the foam in all areas that required to be removed. It might be difficult to blow or vacuum all the bits and pieces and dust out before you fill in the new foam.
The “Acetone” method… It will be difficult to monitor where the acetone will dissolve the foam and I am not sure what happens with the dissolved foam… I do not know if the residue of the dissolved foam is a good basis for the new foam to adhere to.

Please keep us posted. In case you decide to replace the foam core rather than trying to glue them back together – please take lots of pics and post them.

Patrick