Hi lgonzales,
That script will rebuild/expand the original share.war, solr.war and alfresco.war on webapps/ folder.
So, try as much as possible to isolate and keep your customizations on an external jar or elsewhere. In the worst case patch again the alfresco and share folders with your customizations after running your apply_amps.sh or upgrading Alfresco.
When I can't extend a Share's theme resources on a separate JAR or location, I usually have a "patch" folder with the files I simply will add or change against default share's files.