Thanks Man

Solved

Just copy .htaccess and paste it in all salve sites.

If you had created the website to replicate with this .htaccess present, JMS would have replicated it.
As you have created the .htaccess after having created the slave site, this explain why you had to copy it manuallly.

For you information, you can also define JMS template and rules to describe the replicaton of the file.

I did have sef and .htaccess turned on and working in the master site.
the slave does not work

the deploy is at the location domain/joomla/site1

it appears that it is a bunch of symlinks. .htaccess is one of them. and I am not able to overright it.

I presume that If I erase this file and then replace it with a new .htacees with the correct rewrite base, it should work!!

Your analysis seems correct.
I think effectivelly that a specific .htaccess is better than a link.
If you are scare to delete the link, you can start by rename it (just in case where you want to restore it).

I am not sure that you will have to modify the rewrite base.
All depends if you are using with an sub-directory or sub-domain or domain for your slave site.
In case of domain or sub-domain I think (not sure) that you can keep / as rewritebase