So everything is 2.4 defaults, which are:
brong@wot:~/src/cyrus-imapd$ grep '_db"' lib/imapoptions
{ "annotation_db", "skiplist", STRINGLIST("berkeley", "berkeley-hash",
"skiplist")}
{ "duplicate_db", "skiplist", STRINGLIST("berkeley", "berkeley-nosync",
"berkeley-hash", "berkeley-hash-nosync", "skiplist", "sql")}
{ "mboxkey_db", "skiplist", STRINGLIST("berkeley", "skiplist") }
{ "mboxlist_db", "skiplist", STRINGLIST("flat", "berkeley",
"berkeley-hash", "skiplist")}
{ "ptscache_db", "skiplist", STRINGLIST("berkeley", "berkeley-hash",
"skiplist")}
{ "quota_db", "quotalegacy", STRINGLIST("flat", "berkeley",
"berkeley-hash", "skiplist", "sql", "quotalegacy")}
{ "seenstate_db", "skiplist", STRINGLIST("flat", "berkeley",
"berkeley-hash", "skiplist")}
{ "subscription_db", "flat", STRINGLIST("flat", "berkeley",
"berkeley-hash", "skiplist")}
{ "statuscache_db", "skiplist", STRINGLIST("berkeley", "berkeley-nosync",
"berkeley-hash", "berkeley-hash-nosync", "skiplist") }
{ "tlscache_db", "skiplist", STRINGLIST("berkeley", "berkeley-nosync",
"berkeley-hash", "berkeley-hash-nosync", "skiplist", "sql")}
{ "userdeny_db", "flat", STRINGLIST("flat", "berkeley", "berkeley-hash",
"skiplist", "sql")}
So you shouldn't have any berkeley databases at all. It should be
perfectly safe to shut down Cyrus, delete the $confdir/db folder, and
restart Cyrus.