Yes, you will get a performance improvement by going to Linux 64-bit. These days it's not as significant as it used to be, but Linux is still the more performant platform.
The 'gotchas' to be aware of are obviously any file-paths that you have configured in *.conf files. All of the settings and values are the same across all platforms, so it's really just those darn slashes that trip people up.
Your indexed data should also be transportable from one platform to the other, as long as the endians match on both file-systems
