EMILY: You can be so harsh sometimes, and I just don’t know where it comes from or what I’ve done to deserve it.
LORELAI: You did nothing … Mia showed up for a visit and I told her about our plans and she’s talking about selling the Independence Inn and it just wigged me out a little. It’s stupid, I don’t know, but that was our home for so long, mine and Rory’s.
During a pretty standard Friday night argument, Emily and Lorelai actually reach out and express their feelings to each other. (It’s interesting that Emily’s perception that Lorelai can be very harsh is exactly how Lorelai must often feel about Emily).
Unfortunately, whenever Lorelai is honest about how she feels, it often has the effect of hurting Emily. In this case, she has to hear that Lorelai thinks of the Independence Inn as she and Rory’s “home”, and is reminded that it’s the place where Rory grew up. Although she forgives Lorelai for her outburst, and says she understands, she is clearly hurt to hear the emotional attachment Lorelai still has to Mia and the Independence.
In this scene, Lorelai makes it sound as if the Independence was their home for many years, even though they only spent two or three years in the potting shed (as Lorelai said it’s where they lived when Rory was a baby). Possibly as Lorelai proved her worth, Mia was able to move she and Rory into more suitable accommodation in the inn, such as staff quarters. It may be that Richard and Emily only began visiting them at the inn after this point, which is why they never knew about the potting shed days.