Question on whether I have committed plagiarism (modifying paragraphs from an unpublished document sent as email attachment for PhD thesis) Background

My colleague and I are both PhD students (My colleague started about 8 months after me) from the same research group (and share the same PhD supervisor) in a UK university. We were collaborating on a research project with a Prof. 'X' from another university in the EU.

Early on in the project (March 2017), over a phone call, Prof 'X' requested my colleague to provide them with a 1-page project summary to support a small grant application. My colleague and I worked on this at my colleagues work desk for a single afternoon (about 2 hours) to produce this document. Both of us thought out aloud, iterated the words &amp; phrases a few times to write and polish this document. Since we were working on the colleague's computer, after writing we just opened the email client on that machine and sent the 1-page doc as an email attachment to Prof 'X'. 

The document itself contains only 5 paragraphs of pure text. It does not contain any title/authorship or any other information whatsoever (such as header/footer). My colleague signed the email as "Best Regards, A &amp; B". where "A" is me and "B" is my colleague. Later on, the colleague forwarded the same email (with the attachment) to our common PhD supervisor (as an FYI).

As we proceeded further into the project, the involvement of my colleague and mine became intricately interwoven. It soon very became hard for our common PhD supervisor to separate out individual contributions. There was a huge authorship dispute of the resulting paper (manuscript) which lasted 8 months but eventually got resolved, nevertheless leaving my colleague and me in not good terms.

Since this project was important to our respective PhD theses, it became crucial to clearly identify who contributed what. As part of this forensic examination, both of us gave our evidences to our common PhD supervisor, who apportioned the contributions suitably on a high-level basis. It was decided that both our theses shall have a suitably detailed "attribution of content" section for this relevant chapter, and the contents of the scientific reporting shall be minutely scrutinised by our common supervisor to prevent any allegations in the future.

Present Situation

I recently passed my PhD viva. Examiners were happy and the outcome was to submit minor corrections in 90 days time which were to be checked and approved by them. However, just before leaving for Christmas holidays, my PhD supervisor ran my submitted version of thesis in turnitin (against all relevant docs for this project) and found that I had large chunks of text (2 lightly modified paragraphs) copied verbatim from the email attachment.  Our PhD advisor then inquired with my colleague about this, who insisted that the document was entirely written by him albeit with intellectual inputs from me . Therefore, our PhD supervisor asked me to re-write these 2 paragraphs and said they had no choice but to inform the internal examiner about this.

I am really worried. I copied and modified the 2 paragraphs because I thought I was entitled to reuse these words from that email attachment. Did I do something egregious? Am I in deep trouble? I am happy to re-write these 2 paragraphs from scratch, but I cannot afford to lose a degree I worked for 4 years for something little like this.  What are my options if I am accused of plagiarism?
Not knowing the policies of your university, nor of your advisor, it is hard to be definitive in an answer here. However, I'll suggest that you do two things. One is to re-write the paragraphs as you seem willing to do, but also contest the characterization that the original wasn't joint work with you as an equal contributor. If necessary (and possible) make your claim formally, in writing. You don't need to accuse the other student of misconduct, but you need to be clear that you worked jointly. The other student may just misremember the interaction, of course. Best if you have preserved some evidence of course. 

I would also try to get the professor to stand up for you with the internal examiner. 

If you are reporting accurately, then nothing you did was wrong unless the attachment was somehow published and you failed to cite it. That would be self plagiarism and is in a different category than ordinary plagiarism. 

My personal opinion about self plagiarism is that you can copy and include your own unpublished work without citation, but need to cite earlier work of your own rather than just copying. That is to permit readers to trace back and find the complete context of a work. 

However, there is one aspect I'm unclear about. If the attachment wasn't ever published, how did turnitin even find it for analysis? If it was published, perhaps without your knowledge, that raises other issues.