This seems to happen on Cloud Edition v14.12.28 and Desktop v14.12.28, but not on Desktop Edition v14.12.27.
1 - I have an existing inventory item with custom fields. All field are filled up.
2 - Searched for item by its name, click Edit
3 - I edited some fields (a mixture of both default fields e.g. Name, Description, and custom fields e.g. SKU Code)
4 - Clicked Update
5 - Searched the inventory item again. Click Edit
6 - Now all custom fields values for that inventory item are empty. Values for default fields like Name, Description, Sales Price etc are still there.
Edit: This affect creation of new inventory items with custom fields as well.