Sort of. I don't recall the details from the top of my head and can't easily seem to find details, but I think we're seeing some divergence between Typescript's classes and es6 classes, though I think it's mostly syntactic.
Your code will keep working, but it may diverge a bit from standard JS; however everything will keep working, and I'm sure the expectation would be to move over the es6's syntax unless there were semantic reasons not to.
The Typescript authors are involved in the ECMAScript process, so I'm pretty sure that there won't be any surprising huge rifts at least.
I don't know why you're being downvoted. You're exactly right - there are a few tiny divergences between ES6 and TypeScript. In particular, try compiling some classes with Babel's strict compatibility mode and compare the output to TypeScript's output. There are several small semantic differences.
Also, there a few constructs in TypeScript that generate JavaScript code, like enum and module.
THAT SAID, TypeScript is basically ES6 + type annotations, and can certainly be used as such.
I'm hoping that Typescript will be willing to break backward compatibility when necessary to maintain its core advantage of being an assisted version of the standard rather than just another non-standard language. If Typescript gets out ahead of the ES standard and adopts a feature that is presumably coming in ES, but ES changes course and doesn't follow, TS will no longer be annotated, standard ES.
In this case, I'm hoping TS will just make the breaking change and go back to being pure, standard ES plus optional type annotations. Developers who use it would just accept that from time to time, this could happen, but it could probably be made a non-issue if MS just wrote another transpiler: oldTS -> newTS, for people whose choice of Typescript meant they had committed from the start to a system that would ALWAYS require transpiling.
Your code will keep working, but it may diverge a bit from standard JS; however everything will keep working, and I'm sure the expectation would be to move over the es6's syntax unless there were semantic reasons not to.
The Typescript authors are involved in the ECMAScript process, so I'm pretty sure that there won't be any surprising huge rifts at least.