I don't doubt the damage detailed in the past few posts, but baseline info is limited or missing, and analysis of the causes (meaning what actually happened to cause the damage) seems less than perfect.
Some older IR alternators (including models that have been commonly used in homebuilts), if subjected to 'load dump' (like switching off the master while the alternator is under significant load), can have their internal regulator destroyed by the voltage spike. That failure can be either benign (no output), or hazardous (overvoltage).
1st mistake in all cases would likely be: no overvoltage protection.
General bad thought process, partly driven by troubleshooting while we should be flying: having your monitor warn you of overvoltage, and then doing a load dump (?) (turning off everything *but* the alternator), and *then*, reconnecting all those expensive devices to an alternator that you were warned had a problem (???).
While a lead-acid battery will moderate and delay the damage from an OV event, if you disconnect everything including the battery and then reconnect everything, even if you include the battery, the voltage (not a spike; steady state voltage) could well be close to 100V when you repower everything. There's a pretty good chance you'll fry some (all?) stuff before the battery can drag voltage back down to sub-20V levels.
edit: Should have mentioned, many of these older IR alternators, once 'turned on' via their "I" terminal, never stop their output until they stop spinning. So if you switch off the master, even if the alternator is disconnected from the bus it's still making output. Not a big deal *if* the operator understands how it works and the ramifications. But if there's an OV event and no way to open the B-lead fat wire from the alternator (an OV protection relay), then if the bus is powered back up, it'll see the max output from the failed alternator, which can be 100V or more.
With a Brand E.X. battery, you better be absolutely sure you have functioning OV protection, because if the EX decides to take a hike (justified or not), you're almost certain to get a large voltage swing out of *any* alternator that doesn't have OV protection running interference between it & the loads.
Minor tweak to the statement about AEC & removing the battery from the alternator: It's not removing the battery, per se; it's removing *the load*, part of which which may be the battery. But if you've been flying very long, the load is more likely to consist of the normal electrical loads. Once recharged (taking only a few minutes at cruise rpms), the battery is largely just along for the ride. After that point, you could remove/replace the battery terminal at will, and likely never notice that you'd done it, unless you're monitoring an oscilloscope on the alternator output while doing it. You *might* hear a little extra hum or whine in your intercom. (You'd see a max of about 1V of 'ripple' on the DC output of the alternator; far less than the change you get in voltage if the alternator just died, where you'd see an instant drop from 14+V to 12V and falling.) Do understand the difference(s) between disconnecting a battery and turning off the master.
Charlie