To me it is really easier to clean a tank with bare bottom (I have bare bottom tanks and tanks with fine gravel as well).
Considering the bacteria: Bacteria cling to the plants, the sides of the tank, any decoration, the filter and the bottom (mainly the first 2 cm of the bottom where enough oxygen is available).
Do you have a filter running? And can you give any additional information on the tank - do you have plants in it, any decorations (hideaways etc.), how many Axolotls.
I think if you remove the sand at the bottom, the bacteria won't go to another part of the tank (even if you remove it partly). Their only chance would be to move to the bare bottom and there is not so much surface on that compared to any decoration).
So in my opinion you can remove all the sand at once but I would be happy to have another opinion on that.