Is it safe for a toilet cistern pipe to be connected to any othe water pipe?

I am asking because I recently had to have my central heating system changed and the boiler had to be moved, the guy who installed it put in two new pipes that run past the back of my toilet and the cistern inlet pipe is now attached to one of them.

But I have been having some mild sore throats and tummy pains quite regularly since he did this, and I am not sure if this could be the reason.

Hi elligeiac and welcome to The Plumbing Page at AskMeHelpDesk.com

But I have been having some mild sore throats and tummy pains quite regularly since he did this, and I am not sure if this could be the reason. LOL! When all else fails, blame it on the plumber!
Put your mind at ease, Your potty's connected correctly and has nothing to do with your tummy problems. Good luck, Tom