1. How can i remove skills (one or more skill points) that i have already earned and used through the course of the game? I can see a message commenting on the matter from time to time, appearing at the bottom of the screen when loading the game, but it is not possible to read it all as it disappears quickly. Will it cost anything?

2. Can i remove charms i have already invested on my equipment? Will it cost anything?

3. When i remove enchantments from my gear do i have to pay gold? And is this enchantment lost one and for all?

You need to visit a trainer to unlearn your skills. The first is available after you take over the battle tower and become a full Dragon Knight, at a character level in the high teens to early twenties. The cost starts at 5000 gold and doubles each time you unlearn your skills (it isn't terribly hard to get enough gold to unlearn your skills 2 or 3 times).

You can not remove charms once placed in equipment.

You do not have to pay to remove enchantments, though doing so will reduce the value of the equipment. You do not recover any of the ingredients when you remove an enchantment, but if you didn't know it already it will be added to your list of available enchantments (you can get more high level enchantment this way than directly from formula). Once you know an alchemy or enchantment formula you can use it as often as you wish, as long as you have the required ingredients (most of which are relatively easy to get once you have the battle tower; the exception is the relatively rare malachite gem, required for many level 10 enchantments and any level Healing Aura enchantment).

I never bothered with charms.

I also didn't bother with them for a long time and only started using them around the end of the game - since they're permanent, it can be a shame to waste one right before finding some way better gear, thus I found it logical to use them when my equipment isn't that prone to change anymore.