Shubham,
Hi. I will gladly answer your question here.
Let me try to answer your questions in two folds:
1) First let me share the best practice or limitation on multiple apps in SMP 3.0.
Please reference # http://service.sap.com/sap/support/notes/2306453.
2) Each time you do changes into the SMP 3.0 cockpit, it is assumed you have published it accordingly.
For example:
(Following 2306453 document above) I have Work Manager 6.3 and Inventory Manager 4.2 in my SAP Cockpit.
Setup or Given:
Let: Cockpit have two "DIFFERENT" applications (See reference link above for best practice).
SAP Cockpit:
|__SAPWM
|__SAPWM-v1-0-0.agpz (Version 1) - inside the application.zip file (Production).
|__SAPIM
|__SAPIM-v2-0-2.agpz (Version 2 minor 2)
If I want to do a modification to SAPWM version 1 but all I did was modify the Java files in my application.zip (Java/newJava.jar) then I do a load to SMP 3.0 again. I may get what was originally loaded in the shared database (which I do not want because I want the modified one).
Why is this the case? Because there was no identified changes to the key name of the publish.
If you want to see changes then you need an official delta change on the actual name of the version of the product.
In my example above, your published application should now be SAPWM-v2-0-0 or SAPWM-v1-0-1 or SAPWM-v1-1-0.agpz or the system (SAP Cockpit) will not detect a delta change. The incremental number is what is key to trigger that the system will need to replace or load your newly change application into the database. If this step is not done, you may end up loading a prior version from the database back into memory upon restart of the application or you will notice a no change when you restart the SMP 3.0 server.
So my theory is your steps above violates the best practice guide above + you probably didn't know the trick about the incremental number requirement.
We do proactive upskilling for a lot of our customers in SAP Support and this technique is normally discussed in the onsite or web session (try to ask about SAP Customer Outreach from your SAP AE or local support personnel like me - need customer ID # to qualify - technically you need proof you pay for your support maintenance as this is covered in it - topics - SMP 3.0 Agentry administration). It may or may not be available to all regions of SAP yet (If your support staff does not know what it is - ask them to ask their SAP GFM for details about Customer Outreach).
3. You may also try newer version of SMP 3.0 like SMP 3.0 SP10 PL06.
Hope this helps.
Best Regards,
Mark Pe
SAP Platinum Support Engineer