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Okay after consulting the manual and reading up on what they have told you it would seem to me that they are not giving you the best advice. First there is no such recommendation for a transmission service on a CVT for 3000 miles. There is a severe and a normal schedule but nothing saying 3000 miles.
Did you have the actual codes? The transmission runs on a metal belt and cones. It doesn't have a input shaft and a input shaft speed sensor. Maybe he means something else or maybe he's not knowledgeable with this type of transmission.
Let me know.
Ok like I was saying before there isn't really a input shaft. That code is for the drive pulley sensor so maybe they are calling it a input shaft but it's not the same thing.
Here's the flowchart from the manual. You can change it without replacing the whole transmission, if fact I've never replaced a CVT but have rebuilt a few. The start clutch is usually what fails and you have to rebuild the trans and replace it.
If the metal chain/pulley belt broke I could see that for one not making the transmission go in any direction and of course the transmission drive pulley wouldn't move and it may cause a code to store. The engine side pulley may be spinning and the drive not spinning which would definitly cause the computer to note fault. I wish I had it in my stall as I'd love to disassemble it and see if that's the case (belt broke). You can still have it fixed if that's the case but take it to a Honda dealer not a aftermarket shop. You really need a qualified trained Honda technician check it out. With a scan tool in data list mode I could tell you if it's broken by watching the speed of both drive pulleys.