I understand your concern! I purchased ‘Compare It!’ several years ago, and it has saved me countless headaches when upgrading my modified Saratoga and other scripts. There’s a moderate learning curve, but it’s well worth it. One indispensable aspect of this program is that it ignores white space rather than marking every white-space variation between files as a ‘difference’.
Use ‘Compare It!’ with confidence that you can preserve your customizations while you incorporate updates into the script. I run most of Ken True’s updates through ‘Compare It!’ just to be sure I’m not hosing some changes I’ve made for whatever reason.
One caveat is to be sure to inspect VERY carefully the new (Left script) and the old code (Right script) BEFORE you click to ‘import’ it thus overwriting that portion of the old script you’re updating. Some changes are small but they can be important. Fortunately the differences are well-highlighted.