I would like to explain the exact scenario as follow:
There are two CRM instances - one is development (or Dev), and the other is sandbox (or UAT).
I did some changes in the Main form of Opportunity entity (added new fields, and a few more UI changes) in a custom solution in Dev instance. Exported the solution as Managed one, and imported in the UAT instance.
At this stage, Opportunity form appears same in both Dev and UAT instances.
I have created a new solution in Dev instance, and added Opportunity entity again. Did some changes in the Main form of Opportunity entity again by removing some UI elements, and by adding some new fields.
Exported the solution as Managed one, and imported in the UAT instance.
After publishing the changes, I can see that the Main form of Opportunity entity now contains all newly added fields, but also the fields which I had deleted in the Dev instance.
In summary, it didn't delete those fields from the UI of Main form, but just added the new ones.
Could any one please help me sorting out this issue? What could be the possible reason here?
It is by design that changes to forms are merged when importing multiple managed solutions. The MSDN article Understand how managed solutions are merged is a good read for understanding this:
When a solution is packaged as a managed solution the form definitions stored in FormXML are compared to the original FormXML and only the differences are included in the managed solution. When the managed solution is installed in a new organization, the form customization differences are then merged with the FormXML for the existing form to create a new form definition. This new form definition is what the user sees and what a system customizer can modify.