I have an answer for my own questions, based on what NoAlias said. I read the two links and found the following:
Precompiling for Deployment Only
When you precompile for deployment
only, the compiler produces assemblies from virtually all ASP.NET
source files that are normally compiled at run time. This includes
program code in pages, .cs and .vb class files, other code files, and
resource files. The compiler removes all source and markup from the
output. In the resulting layout, compiled files are generated for each
of the .aspx files (with the extension .compiled) that contain
pointers to the appropriate assembly for that page. To change the
Web site, including the layout of pages, you must change the original
files, recompile the site, and redeploy the layout. The only exception
is the site configuration; you may make changes to the Web.config file
on the production server without having to recompile the site. This
option provides the greatest degree of protection for your pages and
the best performance at startup.
Precompiling for Deployment and Update
When you precompile for deployment and update, the compiler
produces assemblies from all source code (except page code in
single-file pages) and from other files that normally produce
assemblies, such as resource files. The compiler converts .aspx files
into single files that use the compiled code-behind model and copies
them to the layout. This option enables you to make limited changes
to the ASP.NET Web pages in your site after compiling them. For
example, you can change the arrangement of controls, colors, fonts,
and other appearance aspects of pages. You can also add controls, as
long as they do not require event handlers or other code. When the
site runs the first time, ASP.NET performs further compilation in
order to create output from the markup. Note
A precompiled updatable site does not allow multiple pages to
reference the same CodeFile class.
I had recently made changes to the site to include 2 aspx pages that referenced the same CodeFile (the same VB code in the background) Each page had slightly different html properties, but needed to have identical CodeFiles, so for my second ASP page I deleted the auto-generated VB code file and then referenced a different CodeFile in the HTML.
As Stated above, precompiled updateable sites do not allow multiple pages to reference the same code-file class. Which is why some of my pages weren't working.
From this point on, I need to avoid using the default checkbox "Allow this precompiled site to be updatable"; It must remain unchecked for my website to utilize the VB CodeFiles referenced my multiple pages.
Conclusion: Multiple aspx pages referencing the same CodeFile need to be precompiled to run correctly. This means the site will not be able to have any changes made to it without re-deplyoying.
