The extent of a loan modification's effect on your credit score first depends on whether your lender reports the loan to the credit bureaus as a new loan or the same loan with changes.
If it's reported as a completely new loan, the changes to your loan balance and the terms of your loan, along with the credit inquiry itself may all affect your FICO score. However, the overall impact of these three factors alone should be minimal. That said, a recent open date for the new loan will indicate that this is a brand new credit obligation, which can cause the loan to have a greater impact on your scores since FICO's credit-scoring model places more weight on recent activity.
If the loan modification is simply reported as the same loan with changes, then there's no need to worry about a recent open date causing the loan to look newer than it really is. Although your credit scores could still be affected by the balance, terms, and credit inquiry, the impact should be minor.
In addition, loan modifications usually require a "trial period" during which you will make your lower monthly payments while your application is processed. Keep in mind that lenders will report you as "late" during this time period, which means this is really when your credit scores will take a beating. For example, a single 30-day late on your credit reports could drop your FICO scores more than 100 points.
