I have the texture plugin "Better Looking Morrowind". It adds nice looking forests to Vvardenfell. It's simple and lovely. Only in Khuul I need to do 'YesToAll'. It is not a serious problem.

flora_tree_jw_ayse_004 is missing in Master file. Current file 'BL-Morrowind.esp'
Cell West Gash Region.

There are a lot of this tree in West Gash. Is there a way to I a way to identify and restore the missing tree in the Master file?

I believe this can happen when one of your other plugins deletes that object. So the master places the object in a cell, that other mod comes along and deletes it, then a later plugin tries to do something like reposition it, and it barfs because you can't move deleted objects.

Search your plugins for the string flora_tree_jw_ayse_004, and you'll probably find the culprit that deletes it. It would be much safer to reposition to some very negative Z postition than delete.

If you need a hand finding the mod, let me know, but a text search tool that can search binary files works good. tes3cmd can work even better to find things, but it's a command line tool.

Edit: here are some plugins that delete flora_tree_jw_ayse_004 from West Gash:
BEx-FM.esp
BE+(1.4) Better Looking Morrowind.esp
Leafy Morrowind.esp
BL-Morrowind.esp
BL-Morrowind.esm
Forested Morrowind.esp

Edit: You aren't by any chance loading both BL-Morrowind.esm and BL-Morrowind.esp?