In Data3Sixty Analyze can you add another CSV/Delimited node to the canvas and configure it to import the data as before. However, switch to the Define tab in the node properties panel, scroll down to the bottom and add a third output pin to the node :

When you run the node there will be a single record on the out3 pin which provides details of the results of the auto-detection process. Please post this information to us.
The characters you indicate in your post are valid for the Windows-1282 code page and ISO-8859-1 character set so there should be no issue handling those characters in Analyze within either a unicode data type field or string type field.
I created a text file with the data you indicate causes the issues (attached). The view of the data in a Hex editor is this:

The highlighted byte is the first e with the acute accent (0xE9). When this data is viewed in Notepad++ the characters are displayed as expected:

Can you also let us know what locale your machine is configured to use.
Attached files
Identified_Lines_w_Extended_Chars.txt