When the CSV file is saved with NumberFormat, the values are not saved to the CSV file. The Text property is saved. This means that you get what you see, for the most part. Formatting a cell in Excel does not change the Value property. Sometimes, that may be what you want I guess.

If that is what you want, we can do that.
e.g.
A2 in one file is 1.555. Formatted to two places is 1.56. Saved as a CSV file and reopened, the value of A2 is now 1.56, not 1.555.

Of course deleting the rows with 0 values in both columns is easily done.