Coverting fp5 to a newer version will not automatically combine them into a single file. The separate files can still be used together, though you may need to check and update the 'External Data Sources' and Relationship Graph for each one so that they point to the correct new files.
To combine them into a single file you would need to import each table from each separate file into your new file, as well as copying layouts, scripts, value lists etc, so yes, would be a lot of extra work.
If you have the time and skills to do it, it might be worth considering a re-build from scratch so as to take advantage of the numerous new features and capabilities in newer versions since v5... You could well end up with a much improved solution :-)
No it does not, it converts the files individually. There is a lot more thought that goes into consolidating multiple files into one. It should not be an automatic reflex. Much of it depends on what the solution does, how much data it has, the desired backup strategy,...
I've converted all the files to fmp12.
I think I am going to re-develop the system as it needs a re-skin and new features adding to it so may aswell start from scratch.
Thanks for the advice.