@newstrings
Skip - what strumming pattern(s) are you using to play the songs? Is this perhaps a factor in your difference between making changes stand-alone vs making changes within a song?
Plus …
When you created your introductory post in February you wrote:
… by which I take it is as Grade 1 Module 2. Six months on you say you are in the middle of Grade 2. I must say your problem may have arisen due to accelerated progress of building your tower upwards without ensuring the solidity of the base and supporting walls are firm and broad.
Go steady and learn the basics fully and consolidate. Here is an overview of Grades 1 and 2:
And here are Justin’s recommended practice routines - to be done several times a week for at least a week for the first few modules and longer than a week as the course progresses.
Realistically, taking an estimated average learning and practice route of 30 minutes per day, increasing (after 3-6 months) to 60 minutes per day on core learning, several times per week, Grade 1 is likely to be about a 6-month or more learning course. More if you really devote time to learning, practicing and playing many songs - as you should.
I wrote this recently in this topic.
Beginner Grade 1 has 75 lessons plus essential consolidation. Each lesson requires at least one day of practice time but by the end of Grade 1, in Modules 5, 6 and 7, I would say that to do the learning justice and really get solid in the basics, each lesson should respectfully be given several days or a week or more, each of the seven modules probably starting at one week for module 1 up to several weeks for module 7. I would even (albeit exaggeratedly to make a point) go so far as to suggest treating each module number as a guide to the weeks required.
Modules 1 to 7 = 1 + 2 + 3 + 4 + 5 + 6 + 7 = 28 weeks. That is more than six months just there.
Grade 2 has 68 lessons. And as the learning ramps up the technical challenge and skill, each lesson and each module will require extended time to really get to grips with. I would suggest a similar approach.
Modules 8 to 14 = 8 + 9 + 10 + 11 + 12 + 13 + 14 = 77 weeks. That is more than a year.
Okay - those cumulative totals are on the high side. But I would rather encourage that over the opposite of not taking enough time and hitting a brick wall of frustration. As many have done. As you have done.
My recommendation - revisit the basics, build a thorough consolidation routine of Grade 1 material with level appropriate songs, be disciplined about chord perfect, one-minute changes, simple strumming patterns in songs (lots of songs), do things slow and correct knowing that speed will take care of itself.
Did I say learn to play simple versions of songs Learn songs, learn a large number of songs [ learn songs, learn songs, learn songs 
] within and at the edge of your skill level and take some backward steps to consolidate.