When opening a solution that contains a custom function whose name collides with a built-in function with full access privileges, display a warning dialog, listing all colliding custom functions, ideally also offering to automatically rename them to resolve the conflict.
The issue (demonstrated on the recent FileMaker 16 release):
In previous version I have used a custom function named UniqueValues.
In 16 equally named function was added as a native function, but with slightly different behavior (mine did not preserve empty values).
After opening solutions where I used the custom function, everything seemed fine. Until I edited one of the calculations using the UniqueValues function. I have not noticed anything, but the calculation without any apparent reason started behaving weirdly in virtually random cases.
An alternative solution might be changing the logic to preserve custom functions over built-in functions in the case of collision. But because that would be inconsistent with previous releases and also would not resolve the issue of developers not noticing the collisions, so I believe the warning dialog is a better solution.
Of course, the automated rename option is potentially dangerous as it would break any dynamic (using Evaluate) calculations even for older versions of FileMaker, but if the user/developer has already upgraded then those would be broken already anyway.