If your custom fields are using contexts, then the values/descriptions of those custom fields are bound to the specific project where that context was created.
Hence other projects could use the same custom field, but have different possible field values, or a different descriptions. But that alone doesn't explain why switching project types would change that.
What project types are you changing between?
The other thought is that this could be a field configuration scheme problem. I am curious to see if the changing of this project would automatically change your field configuration scheme in use here. Those schemes can also control the descriptions that a custom field have on a per project basis. So that seems like the most likely culprit here to me.
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