The Adobe IFilter doesn’t provide a mechanism to supply a password to open a password-protected PDF file, so it cannot be used to open password-protected files.
I was wondering, is there a relatively straightforward way to programmatically retrieve the actual encrypted data inside the PDF file, decrypt it using a standard cryptography API, and then build a new PDF file with the decrypted data?
To open a password protected PDF you will need to develop at least a PDF parser, decryptor and generator. I wouldn’t recommend to do that, though. It’s nowhere near an easy task to accomplish.
With help of a PDF library everything is much simpler. You might want to try Docotic.Pdf library for the task (disclaimer: I work for the vendor of the library).
Here is a sample for you task:
Docotic.Pdf can also extract text (formatted or not) from PDFs. It might be useful for indexing (I guess it’s what you are up to because you mentioned Adobe IFilter)