The command-line document indexing utility docindex.exe (it's installed in C:\Program Files\prs2k\lib\) can be used to schedule document indexing. To find out more view the http://www.methods.co.nz/docindexer/ web page.
For an example of using the Windows scheduler see Scheduling PRSMon Database Compaction and Backups.
Typically you would execute a command like:
"C:\Program Files\prs2k\docindexer\docindex.exe" -i "*.doc|*.pdf" P:\prs2k_data\Documents
This example indexes all Microsoft Word and PDF documents in the P:\prs2k_data\Documents folder and all subfolders.