I'm running Windows 10 technical preview 10049 and I'm running bitcoin-qt from my data hard drive with 1.17TB available disk space. It is a striped volume and due to much data writing and deleting it needs to be defragmented from time to time. Every time I have done this and I start Bitcoin-QT again it gives an error that the database needs to be rebuild what takes ages.
Shutdown Bitcoin-QT cleanly and no reindexing is needed.
The reindexing of bitcoind database is only needed if the application did not have time to properly shut itself down and write all information in its memory to disk.