In the project properties (right-click on the project => Properties => Resource) there is a section for encoding a text file.
Have you configured the encoding here? If not, you have two options: Inherited from Container (which should be the default workspace, in your case UTF-8) and Other, which allows you to select a specific encoding (ISO-88591) ...
I just tested this in one of my projects, closed it and reopened it, and the ISO88591 encoding is still configured.
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