Maybe I am not understanding the issue but if they are no longer in alignment then you just need to finish changing the parts that you are changing and then when you are putting the belt back on and setting the timing then you need to line the timing marks as shown below in these attachments.
Clearly it is easier if they don't move but if they do it is ok as you just need to align the again.
Please run through this info and let us know what questions you have. Thanks
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Tuesday, April 20th, 2021 AT 6:12 PM