Index question for Microsoft folk

Indexing for searches possible large problem.

I am working on a web application using Visual Studio Express and many of my
changes are reflected in code and tags however when I run the application its
as if some features have been frozen in the past.
For example I have a graphic set to a stylesheet which no longer exists on
my hard drive and yet if I refer to that class name the graphic shows up with
all the settings from the previous. Additionally I have datagrids without a
value set to DatasourceID (because I removed it and the datasource itself)
and yet that datagrid when running the application still thinks there is a
datasourceID attached to it which is why it gives me an error when I set
datasource in code. Intrestingly there are no compile errors, no errors when
I breakpoint thru these areas only when the page renders does that problem
begin. The same is true for the graphic.
There are only two things I can think of that would cause this. One, I was
making changes or my project was open while I was doing a search index for
the first time in Vista. Two, I have Atlas dll in the project but am not
using any of the features. I am beginning to think that it’s the first item.
What concerns me (beyond the fact that my project is almost unfixable) is
the functionality issue for search. The first time you hit search in Windows
Vista it starts doing this indexing thing and it does not inform you really
what is going on nor does it advise you to shut down any programs.
I guess the “question� here is this. Could indexing while a another
application is open cause issues with the that applications file?