I haven't a clue what could be wrong. I occasionally have missing pieces in a stitch file when I forgot to create stitches for an object - strangely enough that only happens with line objects or connection stitches -, but I can still save it So I am sorry, but I can't help you.
Sorry, I can't help (that hasn't happened to me) but good luck. Has it just started happening? Hopefully someone will come along soon who knows the answer.
I only noticed it when I tried to save a sample I have reopened & all the save componments are greyed out