No, except for the obvious differences in path name.
As long as the endianness of a system is the same as some other one (which is extremely likely unless you get into VAXes or old IBM mainframes and stuff), the files in the variously configured "indexes" folder are compatible with one another.
I know this for a fact because for some various test systems, I copy an index of about 1.2 GB between 3 different systems - two linux of different distributions and one Windows. Assuming you have the permissions right and the paths set up correctly, those indexes work perfectly well on all systems.
There IS one note - When editing conf files (or xml - anything text based), Windows uses a different line ending than Unix. This is more or less just cosmetic, so that if you open a windows-edited file on a Linux you'll see a lot of special metacharacters ^M at the end of each line, and if you open a file saved in a Linux on Windows, notepad (which until recently didn't understand those line endings) would put everything on one line because ... it didn't understand the linux line endings. 🙂
In all those line endings cases, just search <mytool> convert line ending and that'll probably get you help. If you can't find good results (for like "notepad convert line endings") then use your OS generic ones, like Windows convert line endings. OR, just stop using Notepad and use ANY ONE of the available free text editors that each are a million times better. Notepad++, Editpad, ...
