Hello.
I had a similar issue before in which I came up with 2 solutions after some consulting.
- Replace all the previous files with the new format and keep it that way going forward, Ideally it is better to keep just one type of format for data uploads.
- Create a new version of table and upload the new file in the new version

When creating a new version it keeps the same formula steps and any configuration you might have done.
I personally used the first one since I like to keep just one type of format to my tables, although this means replacing all previous data upload with the new format.
Although overall I don't know why Apptio is not allowing you to select the delimiters, this might be a bug.
Hope it helps.