Site Search and Google Search Appliance Indexing Issue

I have a directory with about 35.5GB of PDF, DOC, and DOCX documents and a subdirectory with 3 documents. I need to search through these documents. The admins created a collection and front-end for the Main directory in GSA but when I run a search, it returns results from the sub-directory only.
One of the guys suggested that the directory is too big to be indexed. Is this true? If so, what is the max size so I can split the directory. What are my options?

My site is ASP.NET
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