In case anyone is interested, here's how I updated the tables successfully:
opcPackage = OPCPackage.open(file);
List<PackagePart> parts =
opcPackage.getPartsByName(Pattern.compile("/xl/tables/.*\\.xml"));
for (int i = 0; i < (parts != null ? parts.size() : 0); i++)
{
PackagePart part = parts.get(i);
TableDocument td = TableDocument.Factory.parse(part.getInputStream());
CTTable ctt = td.getTable();
CTAutoFilter ctaf = ctt.getAutoFilter();
ctt.setRef("A1:I"+reLastRow);
ctaf.setRef("A1:I"+reLastRow);
OutputStream os = part.getOutputStream();
td.save(os);
os.close();
}
opcPackage.close();
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