This is what I'm piecing together from the evidence.
On the day he killed Helen, IS didn't have a story planned beyond Helen and Boris going out locally, either walking or visiting someone by public transport or taxi, and not returning. Perhaps she forgot to tell him she had plans, he is playing on her forgetfulness. He will raise the alarm on Tuesday when he wakes up and realises she didn't come home while he was asleep.
That is the sole reason behind the story about Helen having an incident Monday morning in her Jeep.
It would explain why her Jeep was outside and she wasn't there. I believe he told that story to his sons on Monday evening (I do not believe the 'coincidence' of two sons knowing Helen wasn't at home and not saying a word, one maybe, not both). After that IS has to repeat that driving incident to all and sundry because that's what he'd told J and O. It became a permanent fixture in his account of Monday morning. Police were unable to find Helen or her Jeep anywhere on CCTV or ANPR that morning. Helen's online activity that morning shows IS made it up.
IS panicked overnight about his hiding place for Helen and Boris not being as secure as he once reckoned. What if it was discovered? He had to do something to stop a search and give everyone an indication of where Helen had gone. He thought this was fail-safe, everyone would be thrown off the scent by the Broadstairs story, police would have no reason to search the home beyond anything cursory, looking for her belongings etc.
He has to invent a note because it's too late now to send a fake text message from Helen's phone, and it's also too late to send an email from Helen to him. He knows his sons know Helen wasn't home on Monday night.
While O and J are at work on Tuesday he practices Helen's handwriting and produces a note. "Gone to Broadstairs. Ring me. Love you xx".
He hasn't included anything in the note about Helen not wanting him to contact her in any way. He's written 'ring me'. He's made it a loving note because he doesn't want anyone to think they had argued before she left.
So why does he then start to tell people that Helen said 'don't contact me in any way'? I believe this was first said to John Bailey on Wednesday. He realises (bit slow off the mark) that he hasn't phoned her. He's put 'ring me' in the note looking at it from one angle of creating a harmonious relationship, but not looking at it in terms of it requiring him to act on her request. This is a man who is fire-fighting. As people ask questions he is spurred into action to create a solution. He forgets to destroy the note but doesn't think it's important because he's not expecting police to search his things.
So he dupes J and O first on Tuesday night. Hence the nerves and calling O into his study to tell him Helen's gone to Broadstairs, as if it's some massive announcement. O just shrugs and says it's her place and up to her what she does.
Then John Bailey calls early on Wednesday morning. He's not prepared for that and blurts out 'I thought you would know.' This is an outright lie on the spot, that sees him well and truly bitten on the bum. Whatever he says about Joe and Nick he can't explain saying he thought Helen would have told John she was going to or was already in Broadstairs. The story is that it was unscheduled and unexpected so she didn't give anyone advance notice, and if IS knew Helen had come to harm from J&N she wouldn't have let her brother know she was there for an impromptu break either.
IS has to tell JohnB about the 'Jeep upset', because he's locked into that account now by J & O being aware of it, and John specifically asks him what happened that morning. What stands out is IS can't say why she was upset. This shows he has moved on to another far bigger, better and more relevant story to relate (the note), and is caught out by the question. Prior to the call from John he hadn't invented a plausible scenario and finds it impossible to embellish on the spot. His original plan had already fallen by the wayside. Everyone who knows Helen would not be surprised she hadn't driven herself to Broadstairs because she wasn't a confident driver, so the Jeep outside didn't need an 'incident' any more.
That is how I believe the story evolved by Wednesday.
ETA So why doesn't he write a new note saying 'don't contact me?'. John Bailey asked him to read him the note over the phone. Because he hadn't given the actual wording of this any thought yet, he decided on the spur of the moment to say he had thrown it away.
This became another new addition to his version to tell police on Friday - 'I threw the note away.'
