I would say it doesn't change at all.
The reason you get interest on an account is that you lend your money to the bank, and they can invest it however they want for their own much higher profit. Let's assume the bank can make an average of about 5% per year on their investments. Then it is only proper that they give you at least 2% because, after all, you lent them your money.
For accounts where it is certain that there will be no user-based movement for years because the customer is away on their time-dilated journey, the bank can treat it like a fixed-term deposit account. That meanst that for a certain period of time the bank can be absolutely certain that nobody will touch the money. Meaning that the percentage of the entire fixed-term money sum that can be invested is a lot higher.
So even if you have an account with no movement for 100 years, it is no problem for the bank to pay it back including all interests. For one, interest is added anually (important for the balances of the bank to know how much worth the account is at every point of time). And for another, the bank has easily made a multiple of the interest with their investments.
Some details on banking and interest rates for different account types:
Let's say you are a bank owner. Assume that all your clients together have 1 Billion in savings in your bank. But you don't need to keep that billion in cash ready to pay the withdrawals because you're always getting some deposits at the same time, too. So, effectively you've only got to keep let's say 100 Million in ready cash. The other 900 Million you can invest safely even in long-term investments because it is very unlikely that all your customers suddenly want to withdraw all their cash and nobody deposits anything.
The exact percentage you need to keep in 'ready cash' varies depending on account type. It is a lot higher on credit accounts because you've got to be prepared to have tons and tons of withdrawals and deposits every day -- the fluctuation is very high. So you can safely invest maybe only half the money. On fixed-term accounts, the fluctuation is not very high, and additionally you know the exact date when you need to return the money -- you can safely invest easily 90% of the money. Meaning: you can make more money with fixed-term accounts, so you can give your fixed-term account holders a higher interest rate.
Here, I would be a lot more careful. For one, I haven't yet seen a banking/money system that lasts more than a 200 years without severe inflation / deflation / currency change upsets. For another, there are plenty of banks that go belly-up in such long timespans and you would only get a small percentage of your investments back.
Just imagine you deposited $40 back in 1900. How much would it be worth in 2000? Depends on whether your bank survived the Great Depression. What if you invested it in a German bank? First the hyperinflation in the early 20s, and then either the bank was seized because the owner was Jewish, or it was destroyed during war efforts.
Not to mention that interest rates barely balance out regular inflation even in good years.
So, no, unless you don't need the money I would not leave it alone for a hundred years. If you are lucky, you do get a great increase of money (which is then made a lot smaller by the inflation). If you are not, you lose a great percentage or all of it.
It would be a lot safer to carry your money with you in gold bullions in your space ship and hope that the gold price has increased during your absence...