because I cannot see the area. But, playing the devils advocate, if the roofer damaged the chimney mortar when installing new step chimney flashing, then he/she should be called right back out. If the old step flashing around the chimney had to be removed for some reason and new inserted, then its the roofers resp.
But, if he/she is simply being nice and forwarning you about the mortar chipping of flaking off and falling out due to just age and exposure, then good for him/her.
If its a huge job entailing all the chimney, you have quite a job because of access to the chimney on all sides. If its just several areas, I would just get some concrete latex caulk and caulk it. This stuff is great and dries just like cured conccrete.
You need to get up there and access the situation before you jump into this.
Do it quickly so that if you need the roofer back, you have done so in a timely manner.
Go up there and then get back with us as to what you see.