Background of the problem: I went to France in September 2022 for 1-year Master's in a course in English language but I failed the degree due to very serious chronic health issues. I worked on my health while living in France and applied for same course and the universities which were offering english level courses and was selected in two universities and I chose one. Then I applied for 1 year extension to the visa in July 2023 and I was granted extension till 15 October 2023 on the condition that I will find a permanent accommodation. I found accommodation after searching for 1 month in last week of September 2023 and then I applied for visa extension. The visa office extended my visa till January 2024 as decision making takes time and then in November end 2023, my visa was extended till October 2024 and I was informed of the same on ANEF website, I just had to pay for a €50 Euros Stamp from a burocratic office as a payment and then get a stamp on my passport.
But when I joined the university, the professors told me that they can't give lectures in English. It became very very stressful as there was no help in English and my French level was not upto B2 level since I had applied to English language courses only. I became very depressed to the extent of being suicidal since the courses were not in English and the course incharge didn't even told me earlier despite being clearly asked in April 2023 before applying to their department.
Since I was suicidal, so I decided to drop out of course in 1st week of December and then by third week I decided to leave France permanently and on 18 December 2023, I came back to India and there is a stamp on my passport of the same. I didn't paid the 50 euros permanent visa sticker as I didn't intended to stay in France beyond January 2024 (till the month extension was given)
Now,the problem: I applied to some places for PhD program (not masters) and one place in Czech Republic offered me a place. I am in the process of applying long term visa for the same. How should I prove to the Czech embassy officials that I did not overstay my visa but was only in France till the time extension was given to me? Or I have committed a crime by not paying €50? I already paid visa processing fees in June 2023 at the time of extension of visa?