either way you'll have to bill the customer for all the additional work of upgrading and validating again all the past and present deliverables, so in the overall bill the 2.5K of the super uber duper version of the creative master collection are dwarfed by the bill for the additional work you're billing to your client for their upgrade decision.
it's not like that a version come out every other month, so you're not going to have this problem unless the project is going to last a bit. and the more you did, the more you have to check and validate and get paid for.
on the other hand, if you're taking from start on a project for which you didn't have the software, well, that's your problem. make sure to check twice the next time to not look dumb when the client gives you a file you can't open or work with unless you spend additional 2.5k.
by the way, in every project I worked on, just because you ask, the client knew about the excruciating pain of upgrading the tools mid project and after the initial (and paid for) tool evaluation phase versions were set in stone.
some of the more sensitive clients had data so old and so precious (to it) that they were still using the 3.5 forté version in 2009. (and that's just as bad, but hey, it was their choice, not mine)