WordPress stores content data as text, which is considered either valid HTML or kind of “weak” HTML (without paragraphs markup, which are added by WP in processing). There are third party alternatives (such as Markdown) and embedded options (such as latex), but in principle it is HTML.
The presentational side of HTML can be changed via:
- HTML markup itself
- inline or external CSS
So any case other than external CSS won’t survive content overwrite. And having users write CSS (more so involving tables and things like n-th cells) is unlikely to be any kind of practical.
So as stated this use case is nearly unsolvable in my opinion. The only thing I can think of to preserve changes is forbidding upload on top of existing content.
Stepping aside from content and plain text, tabular data can be parsed and stored in other representation — like array data structures or actual database table. In that case updating it with preserving changes becomes more practical, but by no means trivial (you will need a diff solution capable to resolve the conflicts between edited and new data).