the prestige system will never allow you to lose prestige by “adding” a block (but the amount may be small/large/even 0 depending on the rest of the beacon contents). Removing a block of course, can lose you prestige. Order is not important, no matter what order the blocks are added in, the final prestige will be the same.
Chiselling a block is effectively a remove followed by an add, and the block you add back is not exactly the same (different shape) so its prestige contribution may be more or less than the block that was removed.
Prestige of a beacon is “effectively” synchronous, and there is no delayed system of updating/adjustments.