You can find info regarding upgrading from 5 to 6 and what to encounter here https://docs.mendix.com/refguide6/moving-from-5-to-6
Further it depends on the add-ons your using. So a good start would be to check in the app store for every widget/add-on module if it is compatible with Mendix 6.
Other than the document Corné referred to, you could experience issues when you have excluded documents/microflows. If the upgrade fails to complete, try finding and removing these files (export if you must keep them) before you open your model in v6.
Hi Prem, Also a thing you could do is create a branchline from your project. Update the branchline to mx 6.0.1. IF there are any errors you can see/fix them. Then when you are comfortable enough after, the update in the branch you can update your mainline and know excacly what to do. Good luck :)
One question though. Why are you upgrading to the first Mx6? I would migrate from the last Mx5 to the latest Mx6. So I would suggest doing the migration inmediately to 6.10.10 (the current on the moment of writing). You need to test your whole application due to the upgrade then you might as well doing it to the latest. Saves the hassle of testing multiple times.
Some extra thoughts when doing an upgrade from Mx5 to Mx7. First do the migration from the latest Mx5 to the latest Mx6. Problems you will encounter are widgets that need upgrading or are deprecated and you need to solve this in another way / widget. Second problem will be the theming and layouts you will need to adjust / create. It is sometimes better to start from scratch with the UX builder to recreate the theme from scratch. Then do a test migration to the latest Mx7. We still encounter some issues wiht our model (but that one is quite large) that Mendix will fix in a coming release. So dependent of your application stick either to the latest Mx 6 or finish the migration to Mx7.