What happens to Amy and Lyell in the series shows the connection they have with each other. When Lyell is hypnotised, Amy becomes timid and a shadow of herself, and even Charlie comments that it is as if the spell that took Lyell has captured her as well. Both Amy and Lyell are trapped, Amy in her life in Filbert Street and Lyell in Bloor's Academy. After Lyell is awakened Amy becomes much more lively and self-assured and even plays a part in defeating the Bloors and Harken.
Also, there's the Early-Bird Cameo of the tree that is the Red King, in Time Twister. Charlie sees the tree and goes into the ruin to investigate later, spots some autumn leaves and drops of blood on the ground, and assumes that the blood was from one of the Beast's victims. Actually the blood was the Red King's tears.
The parallels between different characters in the series:
Lyell and Emma: Both Lyell and Emma were put into a deep trance by Manfred Bloor (and on the exact same day) and forgot their memories and identities of themselves. Both were given false names (Emilia for Emma, 'Mr Pilgrim' for Lyell) and were made to disappear in some way (Emma was given a new identity and sent to live with a foster family, the Bloors contrived a car accident to fake Lyell's death). Also, both had a relative who wanted to find them (Miss Ingledew for Emma, Charlie for Lyell) and they were both woken up by an external source (Tolly Twelve Bells for Emma, the King's tears for Lyell).
Mr Pilgrim and Dorothy Bloor: Both live a half-life in Bloor's Academy.
Charlie and Joshua Tilpin: Both have the blood of two magicians running through their veins. However Charlie chooses to be a force for good, while Joshua sides with the bad children.
Manfred's determination (and indeed, all of the Bloors' determination) to stop Charlie from awakening Lyell in Hidden King may seem strange at first, but it makes more sense by the time of the last three books. Lyell is the keeper of the box that contains Maybelle's true will, something that the Bloors don't want to be found. If Lyell awakens the Bloors fear that he will remember where he hid the box and reveal who is the true heir to the Bloors' massive fortune.
Why was Mr Pilgrim unable to resist Manfred's hypnotic power in Charlie Bone and the Blue Boa? Because he'd already been hypnotised and didn't have any will left.
If Charlie hadn't been able to use his wand to break the enchanted belt apart in Blue Boa, Miss Ingledew would be dead. There would be no one to look after Emma. Not to mention Emma would've been consumed by guilt as it was she that had brought the belt home with her.
After waking up from a ten-year-long trance (in which he was practically isolated and alone), Lyell has to have a butt-load of problems that won't go away that easily or quickly. It's possible (maybe even likely) he'd have insomnia, since he rarely slept while he was hypnotised. Not to mention how he'd have to get used to speaking again, after being silent for years.
Manfred and Dr Bloor talking about Mr Pilgrim/Lyell in the abandoned workroom in Midnight for Charlie Bone. Even though they think they're alone they still refer to him as Mr Pilgrim and not Lyell Bone. To them, Lyell Bone is gone, even though he's physically still alive.
When Yolanda corrupted her four nieces, they chose to stay in Yewbeam Castle while James and Paton left. Since Lyell was only two at the time and Grizelda's responsibility, he would have stayed with her in Yewbeam Castle, a place that still evokes bad memories for even Paton. Imagine a kid growing up in a dark, gloomy castle like that with a brainwashed mother, three brainwashed aunts and a great-aunt who is also a powerful hypnotist and shape-shifter. Not to mention the Not Quite Dead Yorath...
In Hidden King, Charlie's reasoning behind freeing his mother first from her bewitchment is that it would be terrible if Lyell woke up to find her gone. However, considering how almost dead Lyell looked a week after Amy's bewitchment, it's possible (and very likely) that he wouldn't have been able to wake up at all if Amy had been transported into the past. In fact, he almost certainly would have died.
If Harken had won the battle on the heath, Amy would have lost her whole family, this time for good. And not only her family—her home as well. They would all have been killed or taken into the past.
In Henry and the Guardians of the Lost, the moment when Pearl leaves Henry in the cafe looks very much at first glance like child abandonment.
After Lyell was hypnotised, he was made to go back home, to his wife who loved him and his two-year-old son, and he didn't even know who they were by that point. Then he received the summons from Grandma Bone and was forced to crash his car into a quarry.
Lyell was best friends with Rufus Raven, who entrusted him with the box containing Maybelle's will. Rufus and his wife died after Lyell disappeared, so Lyell never found out that they were dead until eight or nine years after the fact.