When OWLAPI sees A is subPropertyOf of B, by default, it assumes both A and B are AnotationProperty if A and B is not declared. This is a wrong assumption.
I have attached a testing file. Use OWLAPI to open it and save as a new file. Now, move line 9 to the end and use OWLAPI to open it and save as an another file. By comparing the two saved files, you will notice the difference.
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