I have been struggling with this issue for months but I finally solved it!
# Symptoms
After updating to the latest firmware, v2.02.0, on my Spider V 240 the guitar input produced no sound. The drum loops played and the USB audio interface played but not the guitar input. After a lot of effort I found this is due to a failure programming the wireless receiver code portion of the firmware update. The firmware isn't broken, the firmware update process is.
# Diagnosis
If you long press the home button and see version 00.00.00 for the wireless receiver and n/a for the transmitter then this is your problem! This means that the wireless firmware that is the most important part of the 2.02.00 firmware update did not apply correctly. Since the input jack is used to charge transmitters this code closely interacts with the input jack.
# Solution
Update the firmware using an iPhone! I tried updating using a Pixel 2 Android phone around a thousand times but always got "Update Failed" - (Wireless Prog Err). Remember to flip the switch near the USB inputs on the back of the amp so the iPhone can talk to the amp. When using the iPhone the amp hung at step 8, updating receiver. I let it sit that way for a long time before power cycling the unit. After power cycling everything worked properly again.
# Details
Line6's 2.02.00 firmware exists to prevent the possibility of fire when charging wireless transmitters. Wireless transmitters (G10T family) can be charged using the guitar input jack of Spider V systems. There appears to be something wrong with Spider Remote when updating this firmware revision when using Android. I can only say that it's a problem with Google Pixel 2 phones; it might be OK with others. When doing an update Step 8, the wireless receiver module fails. This failure appears to make the input jack useless but it's actually worse than that.
I thought the input jack was broken on my unit so I bought a G10TII transmitter thinking that wireless input would be nice. I found that didn't work either which led me down this path where I finally was able to update the code, successfully, but only when I used an iPhone.
Factory resets did nothing. Clearing the presets did nothing. Removing the power cable did nothing. Removing USB did nothing. Reinstalling Spider Remote did nothing. A G10TII did nothing. Letting the amp heat up did nothing. Using Spider Remote on a Windows VM did nothing. Loudly cursing did nothing.