The big differences between EJS 3 and EJS 4 is:
EJS 4 adds features to be able to share simulations wordwide.

An issue need to be resolved: What if two user create simulations with the same name.
A standard need to be adopted.
[li] EJS use the ideas of workspace/source:All the EJS XML sources should be placed under  [b]EJS_4.1/workspace/source[/b]
[li]To solve the name conflict problem: all the users should place their source in [b]users[/b] subdirectory under [b]EJS_4.1/workspace/source[/b], each users need a unique user-subdirectory [/li]
[li]EJS adopt two level file structure for users. for example:
[li]I put all my ejs source under [b]users/ntnu/fkh/[/b] subdirectory. [u]ntnu[/u] represents my work place and  [u]fkh[/u] represents myself. (Fu-Kwun Hwang).
[li]Wolfgang: put all his works under [b]users/davidson/wochristian[/b] and he created more subdirectories for different topics.  [/li]
[li]Paco put all his files under [b]users/murcia/fem[/b] [/li]

If everyone adopt the same standard, the conflict problem can be solved much easier. Each user just make sure s/he does not have ejs source with the same filename.

Because I need to know where to find the XML from the jar file user upload to the server.
So I unzip the jar file and check for files under users subdirectory.

Because the files you have upload did not adopt to the above standard. So the code can not find the necessary informations. That is why the simulation did not show up.

EJS add a new feature to help users switch from version 3 to versions.
[li]Please create a unique subdirectory to represent your work place , and create another subdirectory to represent. e.g. moe_sg/lookang (Please do not use [b].[/b] as part of subdirectory name)[/li]
[li]Copy all your EJS sources to your own subdirectory [/li]
[li]Start EJS. You will find EJS console.
[li]Switch to the 2nd tabs ([b]Advanced Options[/b]) [/li]
[li]Click [b]Compile directory[/b] buton.[/li]
[li]Select the directory where you put all your EJS sources. [/li]
[li]EJS will re-compile all the EJS files and generate all the simulations under [b]workspace/export[/b][/li]
[li]Have a cup of coffee and watch EJS working hard for you.
It should work if you follow the above steps and upload your files again.
P.S. You need to copy all necessary resource files (gif/wave) to similar file structure so that EJS can find it.

That was way how I re-compiled aabout 439 simulations one months ago.

I did not switch to EJS 4 for more than one year because I need to re-compile all my simulations.
And I do not have time to do it one by one.
Paco added this features so I do not have reason "Not to switch" any more.
And I am glad that I did switch to version 4 now. There are many new features available for version 4.
There are data tools, Fourier Analysis tool and animated gif generated tool.
And it is much easier to translate string to different language (right click to find GUI options).