For the file you attached, what you're seeing does occur. In MiOS, there are a set of "IR" Services that contain ACTIONS for various AV things like "Volume Up/Down", Channel Up/Down and so on.
These IR ACTIONs only exist for AV-related components, but in the IR world there are also a lot of "non-AV" things (also IR Controlled)
The Transformation process you went through does a map of the IR Actions from SQBlaster/SQRemote to equivalent ones in MiOS. Since MiOS only has IR functions for AV gear, there are cases where there's no equivalent mapping.
In these cases, I simply put in "Placeholder" elements into the I_xxxxxxxxx.xml file, as a "holder" of sorts to contain the Pronto codes. If, at the end of processing the I_xxxxxxxxx.xml file, we've only got placeholders, then the D_xxxxxxxxxx.xml file will not contain ANY Service definitions.
Anyhow, these items need to be "manually" mapped to something in order for them to be accessed via the Vera UI/Scene editor. In the past, I've seen people map these to one of the [various] unused MiOS AV IR ACTIONs. There are a lot of them, so it's fairly easy to do, but just a bit tedious.
Again, this is only required in the cases where you're mapping an non-AV Device to MiOS, since there's no logical mapping for it. For your AV gear, the mappings should be fairly accurate.