I cannot agree with Grable more, wether you chosse a preLinker, or manualy include, definatly dont stick with two sources.
I assume you mean that it would be a lot of work splitting the files. If that is what you mean then please take my advice and do split them.
At its simplest, dont include a file, but include one of two includes, that then includes different versions of the include lists of that file split up.
If you do deside to continue with two/more souces, please ensure its the only possible solution, because nearly anyother solution would be better in the long run, even if the ground work would seem to take longer.
but a few files the changes are so numerous that I really will need to keep two separate versions of them
I assume you mean that it would be a lot of work splitting the files. If that is what you mean then please take my advice and do split them.
At its simplest, dont include a file, but include one of two includes, that then includes different versions of the include lists of that file split up.
If you do deside to continue with two/more souces, please ensure its the only possible solution, because nearly anyother solution would be better in the long run, even if the ground work would seem to take longer.