Different companies are likely to view this differently, some for reasons best known to themselves are awkward regarding any changes. My advice would be to contact the agent who sold you the holiday and also the operator (if the two are different) telling both why you intend to start your holiday late and that you will make your own late flight arrangements. Present it as an announcement from you and emphasize that you will be checking in on arrival, only late, but that otherwise the holiday will proceed as planned. Make sure you get the name(s) of whomever you speak to and make a note of the date and time. Then, in line with what transpires, confirm in writing what is notified/agreed, quoting the conversation(s). It might be a good idea to also advise the resort so they don't assume nobody is coming, rather than relying on other parties doing the communications - this to avoid the accommodation being filled before you arrive.
As you may have heard, airlines don't like people using only one leg of a return ticket because of very complicated pricing - my assumption would be that a package deal would not be looked at in the same way, but you can but ask. You would be unwise to just hope all will be well and stay silent, it is all going to come out anyway so don't let uncertainty spoil the start (and between now and then also).