How to properly change "innodb_buffer_pool_size" value for mysql?
Changing innodb_buffer_pool_size doesn't need you to nuke ib_logfiles. This could easily be the reason for you had to restore the database (*).

Just stop mysql -> change the settings in my.cnf -> start mysql.


  (*) ib_logfiles are holding recovery data, pages which were not yet
  checkpoint to the tablespace. If you remove them without making sure
  you have a clean shutdown you risk losing data and corrupting your
  database.