PLEASE HELP: Student to Skilled Worker Visa

I am a PhD student on a student visa. I have spent more than 24 months studying my PhD.

Currently, i am switching to skilled worker visa. I was outside the UK for the last 103 days (except for one week I came back to the UK) I had severe oral infection and needed frequent dental treatment. All started in April when I went for my annual break then at the end I started having lots of dental issues. I was in constant pain and couldn't eat thus I stayed outside the UK while to continue my treatment. I later came back to the UK to finish some of the on-boarding tasks for the new job and went back to finish the last stage of my dental treatment.

My supervisor was aware that this issue, we had online meetings, was engaged in all my studies mainly writing my thesis, and I recorded our engagement with our educational officer.

Now, I was not aware that I need to inform the visa and compliance team and in turns they inform the UKVI as I changed my study location/ was abroad for too long.

Will my skilled worker visa application be rejected? What do I do? I worked very hard to secure this job. I am too worried to inform the university then they will notify the UKVI and things just get bigger? what do I do?

PLEASE HELP ME