Upgrading to Xapian 1.0
Xapian has supported two main index formats for quite some time: the older Quartz format, and the newer Flint
Up to Xapian release 1.0, Quartz was the default. This is also quite probably what your Recoll index used, except if you had explicitely required a Flint index by setting the XAPIAN_PREFER_FLINT environment variable.
When upgrading an existing Recoll installation to Recoll 1.9, which is normally built with Xapian 1.0 (0.9 is still supported), or after rebuilding Recoll 1.8.2 with Xapian 1.0, you probably want to convert your index format to Flint, which is faster and more efficient (if you were using the default Quartz, you can also elect to just do nothing, the older Quartz format is still supported).
The index format upgrade will not happen automatically, and you will need to destroy the old index explicitely, then restart the indexer (this will cause a full indexing pass, of course, which may take some time, so you may prefer to let it work overnight).
To destroy the old index, you just need to erase the xapiandb directory: typically: rm -rf ~/.recoll/xapiandb, except if you specified a special storage place with the dbdir configuration variable.
If you were using Flint with Xapian 0.9, you must destroy the old index, because Flint had an incompatible format change between 0.9 and 1.0