When doing joins sometimes it appends field names. If there are a lot of fields then it take a long time to do individually. The repoject tool has a batch option. that can be dragged into model builder for use in a script. Something like that would save a lot of time.
Don't know if this helps you but the Help file says the Add Join geo-processing tool honours the Qualified Field names environment so no need to alter anything? Have a look at the help file for the topic Qualified Field Names (Environment setting), there is some example code.
Bump. This has recently become a big issue for us in model builder, and it doesn't make sense to string to together so many alter field tools. There are workarounds if you are OK creating a new feature class, but if you want to modify a specific feature class without duplicating, the alter field needs to run batch.
And for those who are disregarding this because they think just use the "Qualified Field Names" environment; that doesn't work for all tools. Namely, the Make Query Table tool does not honor the Qualified Field Names environment, so it will always append the table name to the beginning of the field name. A batch rename would be extremely convenient when dealing with a dataset that has over 100 attribute fields and all of them now have the table name appended to the front of the field name that needs removed.
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