Does remedial work such as this go on the electrification budget?
Well, that largely depends on whether the existing troughs can fit any more cables in - electrification projects need lots of earthing and bonding cables of various types. RSCs (Return Screening Conductors) typically have the largest cross-section of any cables in troughs (to soak up the vast majority of lineside induced current) so would probably require larger troughs than existing.
I've noticed that in cesses which see a lot of footfall (e.g. limited clearance areas) that rigid plastic 'clip-on' troughs are increasingly being used as the concrete types can crack, with the potential for twisted ankles, animal ingress etc.
Equally, where resignalling is also present, this may be covered in the signalling budget, or the E&P budget where telecomms cables (for lineside/signal post telephones etc.) require upgrade/renewal. It's rarely one team's responsibility.