[1] The NYLE also operated a branch Line between Dayton and Salamanca, also connecting with the Southern Tier Line there, until 1990; the portion south of Cattaraugus was torn out and eventually replaced with the Pat McGee Trail in the early 2000s, while the portion north of Cattaraugus was damaged by floods and landslides in the 2010s and is also no longer operational.

The right-of-way was damaged by the 2009 flooding of the Cattaraugus Creek, resulting in passenger service on the New York & Lake Erie Railroad being suspended until late 2012.

The NYLE was awarded a NYSDOT grant in June 2016 totaling $732,768 to be put towards a rail rehabilitation project that the railroad will embark on between South Dayton and Cherry Creek.

[3] The goal is to replace a switch at the NY&LE's southern end at Waterboro and restore full rail service between Gowanda and Jamestown by 2019, then Buffalo (through a connecting railroad) by 2020.

[7] In August 2023, the NY&LE announced a proposal to introduce rail bike service on the portion of the Dayton-Cattaraugus fork that remains usable.