In his second season with RAF, Ņesterenko's coaching fell one extra point short of earning the club a promotion to a higher division, but the collapse of the Soviet Union ended that dream.
Ņesterenko left RAF in the middle of the 1992 Virslīga season; the club went lost the gold medals to Skonto FC in an extra game.
Ņesterenko signed a 1+1 year deal with Prykarpattya Ivano-Frankivsk which had been just relegated to the Ukrainian Premier League and was hoping to return there after one season.
DAG had a good squad which included Andrejs Piedels, Vits Rimkus, Artūrs Zakreševskis and Dzintars Sproģis.
Almost all the players had left DAG, the club had no financial support the first half of the season, and the only money came in from the transfer of Dzintars Sproģis to Spartak Moscow.
[1] The season in Virslīga wasn't especially successful, but Ņesterenko and his club earned his first trophy in independent Latvia - RAF won the Latvian Cup by beating Skonto FC in overtime in a thrilling match.
In 1997 Ņesterenko was a candidate for head coach position with the newly founded FK Ventspils but Sergei Borovski from Belarus was chosen instead.
After a brief stint of consulting work with Ranto/Miks, Ņesterenko signed for the 1998 season with Dinaburg FC, the bronze medalists and cup finalists of 1997.