Ignite performs delete in a "soft" fashion:
1) When "remove" command is executed, we propagate it to the secondary file system;
2) For IGFS meta cache, we do not remove all records immediately, but rather execute a single "move" operation and move removed tree to a hidden "TRASH" folder.
3) "TRASH" folder is cleared periodically - this is what you see in logs.
Removal of trash content should not interfere with normal operations anyhow, nor should it cause any performance issues. Do you observe some real slowdown, or you are only concerned with metrics summary?