I fully understand. I guess there is no way to alter skim's patience so that it doesn't re-load until (lets say) "2" seconds after a change? As a quick solution, I ended up adding a pdf-copy step and opening the copy of the file instead, which solves the problem in practice (in a non-ideal way).
Thanks for your quick reply. In my case, the working directory is not located under Documents or Desktop, and skim has clearly read access. I think what is happenning is that skim is "not patient" : it tries to read the file while the file is still in a corrupt state (due to recompilation of the pdf), gives a warning prematurely, but then just after a fraction of a section, it loads the fıle correctly. If the warning could wait a bit more or close automatically after a correc re-load, the problem...
I am using a simple vim+pdflatex setup, no fancy integration. Everytime I compile the file, now I am getting this annoying message that requires clicking "OK". My OS is Tahoe 26.3. Skim version 1.7.13. I am not sure when the problem has started exactly. Perhaps something has changed at the OS side? Thanks!