I have been struggling with this topics for months and never had someone at squarespace's support who was able to find a solution UNTIL Conor helped me out 3 days ago.
The issue for me was :
I work on a Mac with numbers while there was no issue opening and saving the CSV file the issue was the format in which CSV file was made by numbers. Resulting in having the document saved/converted with commas instead of semicolons.
Months of stress and manual updated to hundreds of products and no one at squarespace was able to identify the issue !!
However, it is now working perfectly, thanks Conor !
The solution for me was :
1. export the file from squarespace "inventory"
2. "import" the file into Google docs sheets
3. make all changes without removing anything
4. save on your disk
5. "import" the file back to squarespace inventory
ps: I am not changing the name originally exported from the inventory while back to the inventory page
Hope this helps others.