You can make up for the lost time by taking a plane instead of the train.
Literal
Train [of-の] instead [to-に] plane [on-に] ride [by-ことによって] lost time [object-を] make-up-for possible.
A layered causal-means structure. ~代わりに ('instead of ~') takes のに to mark the replacement. ~ことによって ('by doing ~') is a formal 'by means of' structure — nominalized こと + によって. 埋め合わす is the colloquial form of 埋め合わせる ('to compensate for, make up for'). The possibility ending ~ことができる wraps the whole verb phrase as 'is possible.'