Hi Jose Luis,
There can definitely be index incompatibilities when you’re jumping over multiple major versions. It might be easiest to just try and do a test run of dump/restore - usually, metadata issues result in explicit errors.
You should also be able to use Live Migrate to migrate from 3.4 to 4.4 or 5.0 on Atlas. If your final destination is 6.0, then you can easily upgrade from 5.0 to 6.0 once you’re on Atlas. Unfortunately, there’s no direct path from older versions to MongoDB 6.0 via Live Migrate (yet).