Apart from the fact that Shika’s soul might view Seiji as an intruder, there was one greater risk that he had to face.
The "spell" that he was looking for.
There was the possibility of another spell being bound to the amnesia-causing spell located in Shika’s soul in order to prevent its cancellation.
Even if his task was merely to find the spell, not dispel it, there was still some degree of risk involved.
An abundance of caution would be necessary.
…
After Shika woke up and ate breakfast, Seiji brought her to the room where the spell had been prepared.
After entering, the amnesiac girl scanned the entire room, her eyes wide with surprise.
She seemed to realize that something was about to happen, so she shrunk back in fright and stuck as closely to Seiji as possible.