My Fuse software often says "Amplifier Not Connected", when it definitely is. Anyone else have this problem and know a fix?

It's been discussed on this forum. I don't have the energy to look for the thread for you and link you to it...but if you look through the titles, you'll find your answer.
Sorry I couldn't be more help.

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85' Harmony H80T Strat Copy
88' Kay K500 Mahogany
09' Squire Bullet (Partscaster)
12' Standard Strat
13' CD-60
15' Standard Strat
15' T-Bucket 300CE Amber
15' Rogue RA-100D (Beater)
17' Epiphone Ltd. Ed. SG Special-I

there used to be a "sticky" thread with troubleshooting documents. It is no longer sticky, so you'd have to search to find it. But honestly, I wouldn't bother. The thread just has links to troubleshooting support documents and those links are dead.

The message from Fender is clear. Either upgrade to their new Mustang GT line of amps or (in the event that you cannot afford to buy a new amp every 2-5 years) TAKE YOUR MONEY ELSEWHERE NEXT TIME YOU BUY AN AMP.