No worries. I'm glad you like the game!
Every time I go back to this section of the game, I'm surprised at just how spaghetti-fied my eventing is.
The issue was caused by a mismatched progress trigger that made the game think you hadn't skipped repairs when you had. This made Phoebe want to sit and wait for you to finish the last few repairs, despite you having told Ella to take over and her now telling you to talk to Phoebe. It's an easy enough fix, though it won't be implemented until v0.17 since the early access release for v0.16 happened a few hours ago.
I also managed to find a bug in some transfer events that also wanted to argue with how much progress you'd actually made, so now those are fixed for v0.17, too.
Both are extremely specific bugs that I wouldn't have been able to find if I wasn't able to wander around in your save, so thanks for sharing it.
As for a fix, I've got two versions of your save for you.
File1 is set up with the progress tracking on Phoebe fixed for you, so you can continue as though you skipped on purpose if you want.
File2 I just turned off the "skipped" switch so you can continue as though you never hit the skip option.
Just extract the .rar into your save folder (you'll be prompted to overwrite your File1; up to you if you want to keep it or not) and you'll be good to go.
