Great question — answering as the UphillTech team:
First of all, document any such system limitations in case of future conflicts. Some airlines give some guidance on how to handle long names, e.g. Vietnam Airlines: If your full name contains more than 41 characters, please use your middle initial. For example if a passenger's full name is: NGUYEN VUONG TRAN THI KIM NGUYET ANH DUONG MAI, Please abbreviate as follows: Middle name and first name: V T T K N A DUONG MAI Last name: NGUYEN (and in this example, as is typical with airlines, the guidance is incomplete, e.g. it doesn't address long first/last names)
Full answer by Franck Dernoncourt: https://travel.stackexchange.com/a/204426 (CC BY-SA 4.0).
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