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They have no rooms in the house, and the handling room is gone.  I can visit Cleos and Estia at the library and School, but all it does is spend time with them.

If the handling room isn't there then you haven't fixed the house. Make sure you scroll to the right on the nav to see if its actually not there, it was changed (but being reverted in 0.59) to a single height scrollable nav.

Same problem here, I have enter to a point where no girls in the portal + only Estia / Cleos Spending time & Tiale. I was told to go to "indoor garen" but no one is there.

maeve will be there at evening or night at the garden. With the "no girls in the portal" either you've already convinced them like Darth Falcon said, or it is actually a bug.

You have to scroll to the right on the exile nav to see the handling room. The nav was reworked in 0.58 (and being reverted in 0.59 due to it being too confusing)