When manually configuring a Union tool within a module/app, once it's saved, if you go in at any point in the future, and change anything upstream from the Union Tool, it causes an error "[some field name] has been changed and the Union Tool needs to be reconfigured".
This happens even if you do not reconfigure any upstream tools, but mearely access them, physically move them, say, an inch to the left or something like that, etc. Basically if you just "touch" any tool upstream, the Union Tool thinks that the manual config needs to be done over. But even if you do reconfig the Union Tool (either delete it and bring a new one in, or change the current one to Auto and then back to manual), it STILL does not recognize the tool as being correct.
The only way I have found to correct this issue is to click Play, and let it throw the error. Add Select Tools before the Union Tool to change the names to be common, then click on the Union Tool, and switch it to auto. Then click Play again. This can be very inconvenient if you have a module that takes hours (although you can limit your input records).
My suggestion would be to either disable the manual configuration, or add notes to the Help Files stating to use the manual configuration at your own risk, because once it's set and works at the time of creation, you cannot modify any upstream tools thereafter or else it will break the Union Tool and it cannot be repaired -- only choice is to use the Select Tool as I described above