Always nice to say, 'you don't have a problem'!! Those leaves can easily be clipped off at the trunk. Your plant looks healthy! Make sure that ALL of the trunk is out of the soil, that you didn't bury it too deeply.
If that trunk is below the surface, simply remove the plant from the soil, and build/firm the soil that was beneath your plant high enough to support that trunk to stay at the level you've got and not sink into the soil again. Then replace the plant and fill the sides with soil firming gently with each addition of soil.
There should be one to 1 1/2" between the surface of the soil and the rim of the pot. This looks like potting soil. Is it? If not this would be a good time to use potting soil instead of heavy, non-sterilized garden soil. But it looks like good potting soil. Also, if you've put any rock or gravel above the drain hole and under the soil, NOW is a good time to get them all out to use JUST potting soil all the way down to the hole. Lots of people and gardeners still do this practice but the rock/gravel actually makes the drainage worse than no drain hole at all.
Have you seen any flowers or fruit yet? If not you need to change fertilizer so the Nitrogen is less in percentage than the Phosphorus and Potassium percentage numbers. I'd also find a sunnier spot or better yet, get a GOOD grow light. That is only if you want limes. Also, putting this guy out under a covered porch roof during the summer would help any indoor plant. Be very sparing with fertilizer with any plants grown in low-light conditions.
I'm only going by what I can see from the photos. I'm not familiar with this particular lime, the scale is confusing. Could you check the soil around that trunk and the other things I mentioned and send a picture of the plant AND the pot. How did you know your sapling had outgrown its pot? Did you purchase this as a sapling (normal)? Or did you grow via seed? (not normal) These guys are usually grafted to a hardier root stock, not sure about Eureka. I don't see any graft...one reason I am worried about this guy being buried too deeply. Just curious. You've obviously done a great job as he looks so healthy. Cut the leaves off at the bottom when they start dying. I always give TMI, grins...