I have a split mold that we use screws to glue the two parts (doors). However, it was pierced in an area of the flange that is hindering us to make new infusions.

Does anyone have any tips on how to temporarily close these holes and not give air leaks when closing the vacuum bag?

Temporary closure could be with gum tape or bag film and gum tape over the hole.  As long as the cover is leak tight you should be ok.  Alternatively envelope the bag and it is not so much an issue and can be blocked with filleting wax to stop resin coming through. 

Warren Penalver
Easy Composites / Carbon Mods - Technical Support Assistant