Masks have disappeared

I have been working on this project for months. This is a jpg sequence, 11 seconds, 25 fps. Resolution 4272x2848. AE CS4
I have used many masks, 114. I use them to delete the background, it's a complicated scene.
My project has autosave and I also save it myself realy often, every 5 minutes and everytime I exit AE.
The last 4 times I have have opened the project the last 3 masks I was working on had disappeared. I thought I had made a mistake.
The second time it happened again, now it's the third time and it made me paranoid, I guess I didn't dream working on those masks.
(Now im afraid of closing the program again)
What might be causing this? I open the last project using "open recent projects". There is no problem except the missing last 2-3 masks.
Someone help,
Thanks and sorry for the long story.

I'm still not sure what you are saying. Are there supposed to be 3 masks on one layer? If so, when you select the layer and press the M key do you see 3 masks in the timeline? If you do not then I would guess that you did not save your project. If you see 3 masks then selecting them individually should make them show up in the composition window.

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