After you file

the only way to check for sure is to call the IRS. getting through would be the issue

800-829-1040
First choose your language.
Then 2
Then 1
Then 3
Then 2
When asked for SSN do nothing it will ask twice
Then 2
Then 4

"IRS added a letter to my transcripts saying they did not receive a return for me"

is this for your 2020 return?

"The status has been “processing” for 14 weeks!" 

if the letter is for 2020 then the IRS and its computers have gone totally bonkers. 

since it  says processing then they have it so putting a letter in your file saying they don't is totally inconsistent