The problem is actually when it rotates all indexes i.e main and delta indexes altogether it locks the resource file of delta indexes. I moved the rotation of delta indexes with other cron job which is responsible for merging delta indexing.
indexer delta_users delta_users_type
indexer --merge users delta_users
indexer --merge users_type delta_users_type
And rotate only main indexes separately on different cron
indexer --rotate -- users users_type
instead of
indexer --rotate -- all
Hence the separate rotation of Delta and Main index is the resolution.
Thanks