Sounds to me that if Bash is picking up on those .esp's then they are still in the right pane of MO's system. Make sure that when you made, for instance the animals merged merge, you then went back to your SRLE Extended LOTD profile moved the new ---animals merged mod to the specified location, activated the mod in the left pane, then Deactivated all the mods that were merged into that mod in the left pane. Which removes them from the right pane making them unavailable to bash/skyrim, etc. That process is the case for most of the merges short of the few where asked to move .esp's to a new folder in MO/Mods and then deactivate only the new esp folder only leaving the mods themselves active. Long story short, after creating the new merge and activating it in your mods list, deactivated the merged mods, the .esps that were merged should not exist int the right pane of MO's plugins window. Hope that made sense and was the root of the problem.