According to the National Highway Traffic Safety Administration’s website, http://www.safercar.gov, many owners of 2003 to 2005 Honda Civic Hybrids owners have made monotonously similar reports. The owners report that their Civic usually shuddered a bit, usually lost a gear or two and then failed altogether. Some reported hearing noise or a loud bang preceding the ultimate failure. Most often, the vehicles failed when they were parked, however, there were some vehicles that had failures in very dangerous locations (one a major interstate and another the middle of a busy downtown intersection). Fortunately, the owners and their vehicles were not harmed.
Each time the failure occurred, the pattern appeared to be the same or very similar to the ones preceding it. Since the fault was repeatable — actually it was repeating itself — and since the automaker knew it was occurring, Honda should have been able to find a fix (it claims to have found one involving new automatic transmission fluid and a process called Band Burnishing, though, the results that have been shown to date the method may not be working), but it did not. Instead, it is treating each report as a separate incident, apparently preferring to deal with each owner individually. The most common fix that Honda dealers have mentioned is replacing the transmission, a $4,700 option.
The reality of this situation is that Honda’s solution is the only real solution to this problem. The CVT is a robustly fragile transmission. If you treat it properly, change transmission fluid on the right intervals and use the proper transmission fluid then you can expect to get 200,000 miles out of your Civic, or more easily. If, on the other hand, you do not use the special transmission fluid required for the CVT, then you will effectively kill the transmission within 20,000 miles or so.
The technician at the Aamco shop where you brought the Civic was correct. You are going to have to replace the transmission. It is far more than a simple automatic transmission fluid now.