Can large data deletion affect Innodb buffer pool performance?
I restarted yesterday the server with making some changes in the configuration file :
innodb_buffer_pool_size = 48
innodb_buffer_pool_instances = 32
innodb_read_io_threads  = 16
innodb_write_io_threads 8

The buffer pool is used, no more slowness noticed until now (after some refresh).
However, still not understand the reason of the impact of deletion on the buffer pool. Thus I believe that the bad way the app is using queries via ORM is the source of this issue.