I find impossible to update multiple custom functions with a single operation. I use them for various purposes, generating and parsing parameters, making code readable, generating barcodes, handling states and errors etc. They act as little libraries that I insert into every solution I create.
Obviously they start to have their own versioning as they become more complex. And that's where FileMaker begins to be limited. I can't substitute a custom function without losing its references. If I delete it and immediately paste the new one, lots of <function missing> statements appear in the code. If I import the new ones, they get renamed.
So for now the only solution is to manually copy-paste their contents. Which for more than 100 custom functions and 10 files... well, you get it. Now every solution is practically impossible to update. If i fix a bug I have to manually copy-paste into every file (lots of mouse operations, which are slow).
Apparently there is no workaround. And even if the idea is considered, we probably won't see it until FileMaker 18. I'm considering the development of an UI automation solution in AppleScript.