Beth
I checked this out yesterday - sorry for not getting back to you same day.
1) When you run the Offset Surface command and select a single Clipping Boundary, the boundary breaks the triangles around the boundary to create new nodes and then triangulates what was 100% inside the boundary with the additional nodes around the boundary. You can only assign one boundary in the offset Surface command - so that should be as large as you want any parts of it to be later (Step 2)
2) Once you have the offset surface you can assign boundaries to it and use the Add Remove Surface Boundaries to add them to the surface. This puts a filter on the surface and it works as follows
a) The outermost boundary will create an Island from the surface - i.e. data outside it will be hidden.
b) The next boundary inside the outer boundary creates a Hole in the Island - i.e. it hides the data inside it
c) The next boundary inside the hole will form another island
d) The next boundary inside the island will be another hole and so on.
3) So if you want 3 islands only - don't have an outer boundary - just create 3 boundaries around the 3 islands
4) If you want the whole surface but with 3 holes around certain areas then create an outer boundary and add 3 Hole boundaries
This does not corrupt the surface - it is just cropping or hiding the surface triangles from the model so that they don't compute volumes, don't show up in Plan, 3D, Surface Slicer, Section or Profile Views and are not contoured etc. They also will be excluded from Cut Fill Maps etc.
Note: Boundaries applied to a single surface should not overlap, that can cause unexpected behavior / results as it adds ambiguity to the model. So if you are tracking the same lines with different boundaries, be sure that they don't criss cross each other. Note also if your boundary has Arcs in the line, that the arcs will be effectively chorded to create the TIN Models - also if an arc and a lie segment intersect to form a boundary line, it is best to "Break" the arc at the intersect location so that both line and arc get triangulated in the same exact place (chording by breakline approximation parameters for surfaces)
Hope this explains what is happening, if you feel that this is not what is happening to your model, please share the model with me (alan_sharp@trimble.com) and I can take a look for you to see what is happening.