Fellow digital beings,
From a Google search, I found a year-old thread about people having lockup problems while playing through Xenogears.
I don't know if it matters to anyone, but I'm playing the game on my modded PS2 with new, but off-brand memory cards. I haven't tried the game emulated. My file never got deleted, but it did show up as "corrupt data" once in the PS2 browser. I was able to load my (hours behind) file every time it locked up.
I tried to post there, but since the thread was "expired", I thought'd I'd post here.
I believe I have solved the problem.
TWO (PS1) MEMORY CARDS.
The first time it happened to me, it was the first time you fight Ramsus. Then it started happening again; the dreaded lockup. It invariably happened right after the most important cinematics, but would work fine for most other save points.
It always annoyed me that the memory card detection took a while. I never had a problem with the game freezing at a vital save point while I had memory cards inserted in both slots. After a while, I took one out to make the card detection go a little faster. It would work for a while, but then I got to the end of disc 1, and I had to redo the fight with Grahf like FIVE DAMN TIMES because it would always lock up when you save before the disc change.
I even went and bought brand new PS1 memory cards, like some of the other posters suggested, and I realize now that it probably did no good. But ever since I put in my new cards in both slots, the game will save at any save point. The downside is that since both cards are packed full of various game saves, the card detection takes like 45 seconds. That's an eternity when you're at a badass part of the game and you want to see if Fei finally bangs out Elly.
Now that I've dealt with that, I can editorialize a little bit. FANTASTIC GAME. Easily in the league of Chrono Trigger and Chrono Cross, which are the two best games ever made. Coded by Jesus Christ himself, and passed down to the demigods at Squaresoft, who is now one with Enix, the same group of geniuses that brought us the Soul Blazer Trilogy. PHENOMENAL game written by astronomically intelligent people.
I'm looking forward to the rest of disc 2 now, wherein Fei slips Elly the boner, and some other bad guy embraces the glorious Mother of Destruction. And then he gets a robot foot in his ass.