CSV Import and Export problems

I have downloaded the CSV file of my products as all of a sudden my product data at Google merchant was almost disallowed.
So I created my Google path and MPN and other details, saved the CSV file and as I can only upload between 50 and 100 files at a time imported back into the system.

Then we had constant errors, products that were unidentifiable across the screen which took several hours to correct.

After doing all of this I then downloaded the CSV file again and to my horror ALL of the the files (MPN and GTIN etc had been blanked!

Is this Amazon Affiliate updating or a very nasty bug. Anyhow, this site is not fit now and certainly any product file over 1000 will probably not work.

Can anyone suggest a work around as this is a very nasty bug wasting my whole day again?