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Hi Stanislava,
Sorry for the delayed response. Regarding this issue, as a workaround; when you set the custom field the first time, do not change the value. Which means all the flag value should be No, keep it that way then save and close out the project. After that, open it again then you will see all the value are set as no and you can switch them to yes or no as you like and all should work as expected, as the issue only happens when we change the value to Yes for the fist time when we save it.
Please let us know if this works for you.
Regards,
Sheen