Are workspaces created by eclipse for c++ with one OS fully compatible with the same IDE but on another OS or will I have to deal with some kind of issues?
Thanks
In short, no, workspaces won't just work if you change platforms and nothing else due to the locations of libraries, compilers, etc. being different on different platforms.
Another answer here explains how you can use Dropbox's selective sync to keep the platform specific files separate from everything else. Many popular version control systems (git, svn) have an "ignore" functionality that will keep platform specific stuff from being shared.