If most the extra cost is unexpected labor it is easier to eat that cost than if there is a lot of additional materials cost. Presumably you are marking up materials so unless there is a lot of extra material you likely still come out ok on those, just not as much profit as expected.
Always figure the worst case you can think of happening when estimating, even then add a little padding just in case and do look at things like crawlspaces to be sure they are accessible if you know you will be depending on that access.
It is easier to talk customer into a lower price afterward than a higher price.
With rising product prices it may be understandable that things will go up. But if anything went up a significant amount it needs brought up as soon as possible, on just a one or two day project that probably means bring it up at the start or be willing to compromise on cost.