I have just had to re-pot and root prune one of my bonsai, can I now prune it or should I leave it for a while, I re-potted it three days ago and today it's looking a lot better and perked. Also it has tiny cones on it should I remove these or not.

Biddy wrote:

I have just had to re-pot and root prune one of my bonsai...

It's not the best time to repot conifers i'm afraid.
But once done, let it rest for a while.
For pines care:
www.bonsaiempire.com/tree-species/pines

If you are in the northern hemisphere then it was not a good idea, in the southern hemisphere it is a different story. You also don't say what species it is. In any case I would say no do nothing to it until it has recovered from the stress of possibly re potting at the wrong time.

This is the tree I re-potted three days ago, like you say I will leave it a few days before I do any work on it. Do I remove the little cones? I had it given to me so don't
Know much about it.

Biddy wrote:

This is the tree I re-potted three days ago, like you say I will leave it a few days before]

It's a nice tree but overgrown.
You will have to chop it down eventually.

Biddy wrote:

This is the tree I re-potted three days ago, like you say I will leave it a few days before I do any work on it.

Best leave it a few MONTHS after repotting. Trees do not work on the same pace as us?