Hello,
No effect on policies which you have created on SEPM.
However, when you are upgrading to the Latest version, there may be few additional features which would be added to the features / policies.
For example: SEP 12.1 RU2 has Explicit GUP policies in Liveupdate.
I would suggest you to make sure you are aware of these updates and then also make sure you Test it on a Test machine before putting on Production.
Hope that helps!!