"will it trigger an IRS red flag as my reported sEP contribution is only $6,000 for 2024 while the custodian’s 5498 shows $8,000?"
No, it will not trigger a red flag. The $8,000 will be in box 8 of the From 5498 and the IRS knows that amounts in box 8 could be contributions for the year of the Form 5498 or for the year before. There is nothing wrong with making a SEP contribution for 2024 before the end of 2024.
