sorry to mark this as an answer for some reason I can’t comment on this question.
Can you explain more what you mean by “I have a list of posts (with excerpts) being displayed in the page using Short Tags.”? Do you have a list of posts excerpts displayed on the front and some number of short tags in the backend that utilize some plugin?
Without more information I can only point you to the content filter on the WP Codex. You should be able to use that to filter the output before it is sent to the browser.
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