Hello there,
For some reason when I merge the double vertices it changes the model itself. Here is a screenshot with X-Ray turned on and in Wireframe view, before merging the vertices:
When I merge by distance it removes 27 vertices and now the model looks like this:
I am very confused, any attempt to help will be greatly appreciated.
Thanks a lot and have a wonderful day!
Hi @SkrenZz your problem is occurring because you are trying to merge 2 sets of 16 verts (16 from the cylinder and 16 from the dome) all at once.
This has never been available in any of the many versions of Blender Iāve used over the years. Basically, you can only merge 1 set of verts at a time. I know it will seem tedious for taking too long to accomplish what seems like an easy action, but thatās why your model goes into a strange shape, because āallā the verts are trying to merge together at once.
What you need to do is select each set of verts (1 from the cylinder, and the corresponding vert from the dome) and then Merge By Distance. Continue around the object until you have each set of verts merged, and then your object will look fine, and be one whole piece of geometry.
Hope that helps. 
Thank you very much @Miss_B !
I tried your solution and it works!
It should work by selecting all the verts involved and setting/selecting a very tiny distance.
If the distance is too big then more (unwanted) verts are merged.
That should work.
I suspect the distance Blender is looking for merging has got changed accidentally to a very long way. It should be virtually no distance, effectively right on top of each other.
Thatās interestingā¦ I tried doing the whole process again and it worked well this timeā¦ I guess I must have accidentally set the distance which messed it up in my first attempt.
Though I could be wrong, I donāt think 2.79 gives you the option to set a specific distance, so that may be an option from the newer versions of Blender.
Iām definitely going to have to try that out now, even though I usually have one set of verts practically sitting on top of the other set of verts.
OK, Merge By Distance in Blender 2.93.6 defaults at 0.000328ā, which did nothing. I then tried a few other settings, and finally was successful at 0.01ā, and it removed 32 vertices. 
Iāll definitely be making a note of this. 
Then I went to see if Blender 2.79 had that option, though I donāt recall ever seeing it.
OK, no, Blender 2.79 doesnāt have Merge By Distance, so you have to do each set of verts separately as I stated above. Merge By Distance is definitely a very nice improvement.
Then your verts were not really on top of one another. The default works almost all the time. Of course, it depends on how the duplicates came about.
In de old version itās called āRemove doublesā, but still with a distance option.
The distance amount depends on the scale of your model too.
Start slowly. And itās potentially dangerous. Because how to know when it said, 23 verts merged. But mech model technically it should be 22. So always check the mesh. And be able to UNDO.
I started with a Cylinder and deleted the top and bottom faces. Then I added a UV Sphere (a separate item), cut the bottom half off, and then moved it down very close to the top of the Cylinder. I went into Object mode to ājoinā them into one mesh, and I then selected just those rows of verts, and went to Mesh > Vertices > Merge.
I totally forgot about the Remove Doubles option in that menu, AND in the Tool Palette on the left. Iām so used to doing Alt+M for merging in Blender 2.79.
As I mentioned to NP5 just now, I totally forgot about the Remove Doubles option in Blender 2.79. Iām so used to using keystrokes, I always used Alt+M to merge. Now I tried it with Remove Doubles from the Tool Palette on the left and set the distance to the same 0.01 I used in Blender 2.93.6, and it worked perfectly.
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