Charging for small damage that cannot simply be repaired/replaced

[Robert Kruse]

I am renting a room in my house and my current tenant is moving out. She recently caused a small burn in the laminate/vinyl floor in the kitchen. The burn is in the middle of the floor, but is only about the size of a standard Swiss Army knife. The burn cannot be repaired without replacing the entire laminate/vinyl sheet (which extends into the next room). The replacement cost in the flooring alone would exceed the security deposit and I do not intend to replace it at this time since I plan to do renovations in the future. 

In addition to the burn in the kitchen floor, there was a leaky toilet that she failed to inform be of in a timely fashion. She moved in in July, but did not notify me of the leak until mid-October. She says it was leaking when she moved in, but I did not know about it since the leak was small enough to not be noticed simply by looking at the toilet. At some point the water from the leak caused warping in the wood of the vanity. I cannot simply replace this vanity since it is built-into the wall. I am also not inclined to replace the built-in vanity at this since doing so would most likely warrant a complete renovation of the bathroom.

Are there any standard procedures for charging for damages that are not immediately repaired? And how would/should I determine any amount to be removed from the security deposit?

Thanks for any information.