Most companies will place a boat on hold. I would always make sure you have the boat on hold before purchasing tickets. Having said that I have been a owner with 4 different charter companies and it's not unusual to be contacted and asked to change a booking to accommodate a charter. If I had the boat blocked I could turn down the request however rarely did.
I could not at any of the companies block my boat over a existing booking or hold which is as it should be. Just recently I was asked to forgo a sleepaboard on my boat that I had booked to allow a charter booking. The charter company offered to put us up for the night in a hotel at their cost which seemed fair so I agreed to it. There are usually ways things can be worked out.