Meteor package that depends on NPM package. Change NPM package source

I use Meteor v1.x

My Meteor package depends on NPM package.

What is the best way of changing a source code of NPM package that my Meteor package depends on? I can see that Meteor stores NPM package sources under

packages/my_package/.npm folder

What if I change something in this folder? Will my change be persistent if a new version of NPM package released?