WinterCG is trying to help standardize web APIs to address these concerns. So one strategy when writing server-side js is to stick to standard APIs as much as possible.

If you do want to leverage runtime-specific code you can isolate that code in separate modules, so if you ever do need to migrate off a particular runtime it's easier to identify/replace that code.

Ultimately it's all JavaScript, and since most of these runtimes are open source even if they're abandoned we might see community forks. Though even if your chosen runtime is completely without support, I don't see a migration off being an extremely urgent or difficult task for most projects.