I spent more than a week to convert the whole project and came to a solution below:
First, de-integrate the cocopods dependency from the project and then start converting the project to the latest swift version.
Go to Project Directory in the Terminal and Type:
pod deintegrate
This will de-integrate cocopods from the project and No traces of CocoaPods will be left in the project. But at the same time, it won't delete the xcworkspace and podfiles. It's ok if they are present.
Now you have to open xcodeproj(not xcworkspace) and you will get lots of errors because you have called cocoapods dependency methods in your main projects.
So to remove those errors you have two options:
Once all the errors get removed you can convert the code to the latest swift version.
Sometimes if you are getting weird errors then try cleaning derived data and try again.