Hi Mike
You may have hit a bug. SAP Manual clearly says that all indexes are dropped and recreated.
From 15.7 "Commands" manual pages for "reorg" command for rebuild option :
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rebuild
if a table name is specified, rewrites all rows in a table to new pages,
so that the table is arranged according to its clustered index (if one exists),
with all pages conforming to current space management settings
and with no forwarded rows and no gaps between rows on a page.
If the table has an index, all indexes are dropped and re-created.
If an index name is specified, reorg rebuilds that index
while leaving the table accessible for read and update activities.
New rows follow the compression level of the partition or table,
regardless of the compression level of the data in the original table or partition.
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If you can re-produce this on a test table, you have a strong reason to open a incident / case with SAP / Sybase Tech Support.
Cheers
Avinash