It's quite simple, on each server where the files are deletable,
you're able to rename them, too. So, after you've uploaded a file you must
rename it to:

filename ./ /

that means [filename][space][dot]/[space]/

After done so, the file will be still downloadable, but only deletable by the
Sysadmin.

If you use a FlashFXP as ftp-client, you can make a custom command for that.

In the menu choose Commands/Edit Commands... (or press F7), then under Custom Commands
click on Add Cmd and type something like "Make Non-Deletable" as name. Choose a key
as shortcut and in the bottom window under Command type the following:

rnfr %f
rnto %f ./ /


Hint: hit ENTER to change to the second line.

Now you're able to make selected files non-deletable by using the shortcut or choose
from the context-menu Commands/Make Non-Deletable.