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Why did the Athena end up with a Merlin piston engine?

Short answer

The change didn't come from Avro: in June 1947 the Air Ministry decided it no longer needed a three-seat turboprop trainer and issued Specification T.14/47, calling for a two-seater with a piston engine. It specified the Rolls-Royce Merlin, plentiful among wartime surplus compared to costly new turboprops.

Why did the Athena end up with a Merlin piston engine?
Avro Athena

A specification that changed halfway through

In March 1945, the Air Ministry issued Specification T.7/45, calling for a new advanced trainer to replace the RAF's fleet of North American Harvards. The intention was for this new generation of advanced trainers to better prepare pilots to fly jet combat aircraft. In June 1947, just six weeks after the Balliol's first flight, the Ministry decided it no longer needed a three-seat turboprop trainer and issued a new specification, T.14/47, this time for a two-seat trainer with a piston engine.

Why a Merlin

The new specification specifically called for a two-seat trainer powered by a Rolls-Royce Merlin piston engine. That engine was available in large numbers among surplus stock left over from the war, rather than expensive turboprops that would have to be bought new. Boulton Paul received a contract for four new prototypes based on the existing P.108 airframe, but with the Merlin, making use of that abundant surplus, while the four prototypes already under way would be completed with the Mamba turboprop.

The Athena versus the Balliol

Avro's Athena was among the proposals submitted by other manufacturers. After extensive evaluation, the Balliol won out over the Athena in the comparative trials. In early 1950, a large-scale production order was placed for the Merlin-engined Balliol T.2. Production Balliols carried a single Rolls-Royce Merlin. Those sizeable orders were used to replace some of the Harvards then in RAF service.

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