it does not stop you, but can and does cause problems with some software and games written for 1.3.
you have a few options
If you have a harddisk you can use whdload(available on aminet) to install the games to harddisk, these installers usually fix problems with running 1.3 games under 3.1
depending on which amiga you have you can get a kickstart switcher so you can two sets of roms in your machine and swap between the two.
if you have an acccelerator in you amiga made by blizzard you can you a program called blizkick to install older kickstarts in its memory
or the final choice you can use utilities which try and degradde your machine to 1.3, these ten to have limited success
