I opened a CSV file which uses semicolon as field separators and I used the default setting for "Separator Options" in "Text Import" window, which has Tab, Comma, Semicolon checked. Then I saved the file with Ctrl+S. The file now uses comma separators.

Workaround:
In "Text Import" window, choose only the correct separator for the file. Deselect all other separators. Saved file will have right separator.

Proposed soluation:
Calc should remember the separator that was in use on import. I recognize this isn't possible when several separators are chosen in "Text Import" window. However, Calc could determine if only one of the chosen separators were really used in file and if it was, use that character as delimiter on save.