Steps to recreate it:
Enter the txt as seen on the screenshot
[1] Book A
[1] Book B
[1] Book C
[1] Book D
Open Columns++ Search and enter regex to generate the sequence
Click Replace All, which should perform 4 replacements
Go back to the text and click Ctrl-Z to undo
Go back to Columns++ Search and click Count - It gives 3 matches instead of 4
If I select all the text, copy and paste it again and go back to the Columns++ Search and click Count - It gives 4 matches!
So, if undo is used, from that point on, first line is ignored by Columns++ Search
Image 1 is what I described. Image 2 is if I do all that starting with a blank added at the top confirming that the first line is ignored.

Steps to recreate it:
Enter the txt as seen on the screenshot
Open Columns++ Search and enter regex to generate the sequence
Click Replace All, which should perform 4 replacements
Go back to the text and click Ctrl-Z to undo
Go back to Columns++ Search and click Count - It gives 3 matches instead of 4
If I select all the text, copy and paste it again and go back to the Columns++ Search and click Count - It gives 4 matches!
So, if undo is used, from that point on, first line is ignored by Columns++ Search
Image 1 is what I described. Image 2 is if I do all that starting with a blank added at the top confirming that the first line is ignored.