No problem for the last so many months I've been doing this.
There's a problem with Stencyl that you can't have two projects opened at a time. So I use build 8XXX of Stencyl version 3.3 and buld 9170 of Stencyl version 3.3. If I need to have two projects opened, I'll open one project in one Stencyl version.
This way, if you need to copy any code between two projects, you could do that seamlessly as well. Never gave me any problem.