I have an issue where

nf-core pipelines lint

passes locally (nf-core tools 4.0.2), but

.nf-core.yml

specifies 3.5.1. Can I bump this manually to 4.0.2?

I wouldn't. If you do a template update it should update it. The value should really be indicative of what template version you are on imo

Ok, thats kind of what I assumed; I will merge the TEMPLATE then