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Introvert,
You wrote that your goal is "modification of one object and rebuilding all the indexes". What indexes are you referring to?
If the indexes that you want to rebuild are the indexes that indicate where each object exists in the file, then that *is* the XRef table.
The XRef table is carefully documented in both the 1.3 and 1.5 specs. If it is damaged or not present, Acrobat will try to scan the file and rebuild the XRef table, but this is not something you should rely upon, because that scanning/rebuilding will not always work. Some people modify an object directly without rebuilding the XRef table, and this poor man's solution seems to work great, and they don't know why others warned about the complexity of PDF files. But then some files are produced that Acrobat cannot scan and rebuild the XRef table, and the solution fails.
There are multiple libraries that can modify a PDF file, and --please forgive me for being harsh-- if you cannot find a reference to the XRef table in the PDF Spec, then you are quite likely getting in over your head to try to write a library yourself to manipulate a PDF file. You may be able to write a simple solution to modify a PDF object, and it might work all of the time. Or it might work some of the time, and then you will have trouble.
PDFZone and PlanetPDF both list many libraries for manipulating PDF. If you tell us more about what you are trying to do, someone could recommend a particular solution. Tell us: Platform and language and what you are actually trying to do. Do you want to change text on a page? Move a form field? The more specific you are, the more we can help.
Regards, Dan-Ari
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