I've deleted some rocks near seaside cause IMO they look terrible, they are no longer visible in Construction Set, but when I try it ingame damn rocks are still there, when I try to get closer, they disappear, and when I'm getting away they appear again. I've tried both loading and starting new game and got same thing. What could it be?

You usually can't delete objects added by a master file (ESM) using an ESP. In addition, the rocks exist in your saved game, so you'll need to clean your save (with Mash) before they'll disappear. The best solution, though, is to move them down underground instead of deleting them. You can move master objects from a plugin, just not always delete them.

The description of the problem directly correlates to MGE, and distant land static generation vs. them being loaded (or deleted) in a mod. What is happening is that MGE has generated the rocks from the Morrowind.esm in the distant land, so even though they're not technically present in the game, they appear when the distant land statics kick in.

So it's like, I can't use distand land and mod at the same time or I'll get this stupid effect, right?

You'll have to ask in the MGE thread. There's a way to make exceptions, but I don't know myself exactly how you would do this. The people in the main MGE thread would be able to answer this question.

You might try peachykeen's suggestion to move the rocks under the ground instead of deleting them, and then load the mod when you recreate your distant statics.

What revision of MGE are you using? Have you regenerated distant land/static files to include your altered ESP?

A-ha. Good catch. Looks like it helped, rocks finally vanished
Thanks