This is my number one tip for dealing with notes.
Start at the end.
If you're given a list of time-coded changes to make, start at the end of the list and work backwards through them.
Because then none of the preceding timecode values, attached to the preceding notes, should have been effected by your changes.
This means that everything will stay in sync.
If there is a change that will make a difference to the other earlier timecodes - “Lift this and put it earlier”, for example - then leave this till last, if you can.
Did you forget to do this first?
Hopefully you also remembered to duplicate and increment your timeline/sequence before you dove into the changes.
If this is something you regularly forget to do:
a) you're not alone
b) help is available