A student used the abbreviation RoE for 'Rules of Engagement'. Thus, it is quite correct to write 'The RoEs were changed'. But what is a single rule of engagement was changed. Can one still use 'RoE, treating the abbreviation as a singular noun: 'It was seen that one RoE was being abused'?

Generally RoE [or ROE] stands for 'rules of engagement', i.e., the plural noun, but it CAN represent the singular as well: 'rule of engagement'.

On this basis, the way to distinguish between the two would be to initially define it as singular: 'rule of engagement (RoE)'. This then allows for the plural use - 'RoEs' - perhaps also expanding this abbreviation on first use: 'rules of engagement (RoEs)'.

If you think RoE should always be a plural noun then, as you suggested, use the wording around the abbreviation to make this clear: 'It was seen that ONE OF THE RoE WAS being abused.'