If you look at IsoSkeyAcadBlockMap.xml in the /Isometrics/ folder of your project, that has the mapping for the SKEY's to the ACAD block it will draw in Isometric.
The default shows this: <SkeyMap SKEY = "BE??" AcadBlock ="Elbow"/>
It means that anything with an SKEY starting with BE and ending in a wildcard will draw the Elbow symbol. To change this, you will need to add your own symbol in the Isometrics settings, and change the AcadBlock entry above to point to the name of your new block.
So lets say you draw an elbow with flanges on it, and called it "ElbowFlange", so the above line would need to change to look this this:
<SkeyMap SKEY = "BE??" AcadBlock ="ElbowFlange"/>
To add the new symbol, go into the project properties, and open up the Isometrics options, and in the last dialog for Isometrics (where you setup the Title Block" there is a button for Isometric Symbols. This is where you add the new Iso block symbology. Draw it as a plan flat 2D item, just look at one of the other Elbow blocks, and give it a new name with the symbology you want.
If you want screenshots, let me know.
Firstly, thanks for your reply.
I did what you said and it worked. But I still have a little problem, the connection between the flanges (flanged elbow and pipe fixed length) displayed in the isometric is being shown in different planes, see attached file.
How can I fix it?