With a bit of luck, you should get PDF/A right out of LaTeX.
A working PDF/A validator that can point out exact problems is here: https://github.com/mff-cuni-cz/cuni-thesis-validator
Common PDF/A problems include:
- imported PDF pictures that are not PDF/A.
- the used font does not support PDF/A (including the fonts in imported pictures). See https://martin.hoppenheit.info/blog/2018/pdfa-validation-and-inconsistent-glyph-width-information/ for a very ugly case.
Solutions:
- use `pdfa.sh` to convert PDFs to PDF/A-compatible form the "hard way" (although this does _not_ retain the PDF/A metadata mark, see comments in the script).
- read the commentary by Martin Mareš (that describes most of the common problems) here: https://mj.ucw.cz/vyuka/bc/pdfaq.html
- use `pdfa.sh` as a last resort for `thesis.pdf` if everything other fails
Parts of the code (esp. the title page) are based on the original template (available from the faculty website) by Martin Mareš, Arnošt Komárek, and Michal Kulich. (Thanks!)