Are the paragraphs in threaded text frames in InDesign, or are they each in separate stand alone text frames. If the later, that could have caused them to separate.
The text was threaded. I removed the thread after testing the first output to pdf when the issue first showed up. I have also tried taking paragraphs pasting them into text editor to remove formatting and pasted them into a new text box and the same issue happens
I can't replicate the issue.
This isn't the whole problem, but it looks like you may have empty paragraphs between each paragraph. If that is the case, remove them and use Space Before and Space After settings.
Do you have special characters in your text that are being used to create line breaks?
Are you using the Articles panel to sequence your text?
When you File > Export to PDF, are you choosing Adobe PDF (Interactive)?
In the export dialog box, do you have Create Tagged PDF and Use Structure for Tab Order turned on?
Have you applied a paragraph style to your text, and if so have you assigned a PDF tag to the paragraph style?
I don't know what your InDesign document layout looks like, but the simpler the better. Usually the more it looks like an MS Word document, the better the accessible pdf turns out.