Thanks for the suggestions. I tried a small test by converting a file to DOS formatted line endings using Geany, then tried the R-E search and replace. I found this did not work in Windows, but does in Linux. After a closer look it seems the Linux version will prompt and ask if you want to continue from the beginning, "End of file reached. Continue searching at the beginning". Whereas in Windows it never give you the prompt. I then retested in Windows starting from the top of the file and it worked fine.
Also, I swear this conversion on the save used to work ~2007/2008. I think it is also assumed that the "Save as" option for selecting the format would force a conversion of the line endings. If no conversion is made, then what is the point of having this option for a "Save as" feature?
Thanks for the support.