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Can you start a sentence with 'That is, unless' when the sentence is a clarification of the previous sentence.

If farmers and vendors know how to prevent bacterial contamination and how to wash produce properly, then even street food will be much safer to eat. That is, unless you take into account the amount of fat and sodium that it often contains.

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Starting a sentence with "That is," is common and understandable in casual writing but would be considered unacceptable in more formal (e.g., academic) writing because the resulting sentence isn't a complete sentence. A preferable alternative would be to replace the period with an em dash or enclose the second sentence in parentheses:

...much safer to eat―that is, unless you take into account the amount of fat and sodium that it often contains.

...much safer to eat (that is, unless you take into account the amount of fat and sodium that it often contains).

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This is a perfectly acceptable form, even in formal academical writing. Replacing the period by an em-dash to make two sentences into one in no way improves the flow of thought nor the grammar. Sentences are intended to be read as part of a paragraph, and need not stand on their own.

However the construction: "X. That is, unless Y." often merely adds words without adding much to the meaning. Often a simple "Unless" can be substituted with no change of meaning. It is (I think) most useful where it indicates an ironic footnote to the previous sentence, as it does in the example in the question. When it means just "on the other hand", it should probably be edited out.

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