It is important to understand that when STIL reads in a a VOTable document, it creates one or more StarTables from one or all of the TABLE elements and then discards the document. This means that information in the document's structure which does not map naturally onto the StarTable model may be lost. Such information currently includes GROUPing of PARAMETERs and FIELDs, and the hierarchical relationship between tables arranged in RESOURCE elements. The meaning of references from FIELDs to COOSYS and TIMESYS elements is preserved, though the textual details may change. It is possible that some of this lost metadata will be stored in some way in VOTable-type StarTables in the future, but some loss of information is an inevitable consequence of the fact that STIL's model of a table is designed to provide a generic rather than a VOTable-specific way of describing tabular data.
If you want to avoid this kind of data loss, you should use the custom VOTable document parser described in Section 7.3.2, which retains the entire structure of the document.