When you delete a Custom Form question, it will delete the data associated with it. If your event has already taken bookings, so that you don't loose this data, it is recommended that you deactivate the question rather then deleting it.
Deactivating the question will remove it from the booking screen, but still allow you to access the data collected previously via reports.
To deactivate a Custom Form question:
From the left menu, under Additional Information, select Custom form (data collection)
Next to the Question you wish to edit, click Edit
Under the field Question Status, select Inactive
Click Save