Let's say you have published some projects with NeoLoad 4.1.xx. Then after some point, you are now using NeoLoad 4.2.xx. The projects stored in the Team server are still in 4.1 format not compatible with 4.2.
That "migrate remote project" will migrate your 4.1 project to 4.2. Before using that option, make sure that all your NeoLoad controller have published their modifications. In other words, the projects on the Team server have to be up to date.
I would suggest you to tag your older project version in case you would like to use them later on.