After having disk problems (it looks like), I rebooted the system and found that Couchbase had automatically deleted all the indexes. I found no way to restore only the backed up indexes and had to manually recreate the indexes - this is an extremely strange database behaviour, was it not possible to handle this case in a different way instead of deleting all the indexes?
Web console log:
Cleaup done for index xxx, partition id 0.
Detected storage corruption for index xxx, partition id 0. Starting cleanup.
Repeat and delete all indexes
Indexer log:
[Error] plasmaSlice:NewplasmaSlice Id 0x693ac0 IndexInstId 12332122332123322123 fatal error occured: Unable to initialize xxx.index\mainIndex, err = Bucket/xxx/Mainstore#12332122332123322123:0 : fatal: read failure in recovery: EOF
[Error] plasmaSlice:NewplasmaSlice Id 0 IndexInstId 12332122332123322123 PartitionId 0 fatal error occured: Storage corrupted and unrecoverable
[Info] Bucket/xxx/Backstore#12332122332123322123:0 Plasma: Disable page eviction before reaching quota.
[Error] Indexer:: initPartnInstance storage corruption for indexInst
…
Indexer::initFromPersistedState Starting cleanup for PartitionId: 0 Endpoints: [:9105]
Indexer::forceCleanupIndexPartition 12332122332123322123 0 mark metadata as deleted
ClustMgr:handleCleanupPartition&{{9876499879879879879 xxx plasma Bucket acb327acb273acb19287acb390acaacb false [field] N1QL SINGLE [false] false false false 0 false 0 {true 0 0 0} 0 0 0 0 0 0 0 0 0 0} 12332122332123322123 0 0 true}
…