As was mentioned in an early comment, there is no single preposition that should be used at the exclusion of all others. This is a case where a small handful of prepositions could be used, and quite a few would sound idiomatic and grammatical. For example, it you want to emphasize that the problem was resolved while the customer was on Skype with the technician, you could say any of these:
- ...resolved over Skype call
- ...resolved during Skype call
- ...resolved via Skype call
- ...resolved by Skype call
- ...resolved on Skype call
- ...resolved through Skype call
- ...resolved with Skype call
whereas if you simply want to emphasize that, after the Skype call was over, there all issues had been resolved, you could use:
- ...resolved after Skype call
Why do so many prepositions work? Mostly because many prepositions are flexible words with multiple meanings, some of which are overlapping, especially in the context of communication. For example, if you are on the telephone, then information is being shared over the phone line during the conversation, that is, while you are conversing with the other person.