I'm a tad confused - what did you expect to see in your application, other than the values you actually loaded from the file? How would Qlik know about any other potential values? Are there other tables/files you're loading from?
Keeping the existing values in the application as is, just appending the ones in the file. There are several tables loaded into the application; transactions, products, customers etc. So with my script Year and Week are actually replacing what's in the application already? Sorry for my lack of knowledge here.
What you're describing shouldn't typically happen, but it may result from any number of things:
1) Other tables may be attached to these tables/fields via specific JOIN or KEEP statements
2) There may be WHERE EXISTS conditions in your other loads based on these fields
3) There may be permissions (Section Access) based on these fields
When you add a field which name-matches an existing field, Qlik will automatically create keys (joins) based on these fields, but that doesn't actually eliminate any values already there. If you don't want these joins created, you can avoid them by renaming the fields as you suggested. If you do that, you may end up with an "island table" that isn't joined to any other tables, though - that may or may not be what you want.
Thanks for clarifying. There's a binary load of another application into the one I'm working on now and that's including this Calendar script (attached), not sure if it explains why I'm facing this issue. The Excel data needs to be joined to the existing data, not beeing an "island table".