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So if I say "install fs3:" will that erase all the files I copied from the USB stick?
The "Install" command (all the versions which shipped with Workbench 1.x, 2.x, 3.x and also 4.x) is safe to use with storage devices which aren't df0, df1, df2 or df3. The "worst" that could happen is that the "Install" command will complain with the somewhat unspecific error message "object is of the wrong type" (what is that "object"? it's the device you wanted to install a boot block on) or just printing the command template ("Usage: INSTALL [DRIVE] {DF0:|DF1:|DF2:|DF3:} [NOBOOT][CHECK]") again.
The "Install" command versions which shipped with Workbench versions 1.x, 2.x, 3.1, 3.5 and 3.9) are restricted to df0-df9 and (2.x onwards) cc0-cc9 (for the Amiga 600 and Amiga 1200). If you had unwisely picked any of these storage device names for your USB stick partition name, then strange things would have happened. These "Install" command versions make assumptions about the storage device driver (df0-df9 will give you "trackdisk.device" and cc0-cc9 will give you "carddisk.device").
Things are a little bit different for the "Install" commands which shipped with AmigaOS 4.x, 3.1.4, 3.1.4.1 and 3.2. The 3.2 and 4.x versions will do their utmost to verify that the storage device to install a boot block on makes sense. For example, any floppy disk drive is configured to feature two reserved blocks at the very beginning of the storage medium which are not available for file system use, and the disk covers the entire storage medium (i.e. the "df0:" device configuration includes both the very first and very last cylinder of the medium: this is never true for the partitions defined by an Amiga RDB block created by HDToolbox, etc.). These are the basic criteria for a storage device which could make use of a boot block: the boot block goes into these two reserved blocks (there must be enough room for at least 1024 bytes of floppy disk boot block code) and should not accidentally damage any data stored there. Otherwise you might end up knocking out the partition, etc. information stored in an Amiga RDB block which defines the layout and properties of all the partitions on the storage medium, and then some.
What about the 3.1.4 and 3.1.4.1 versions then? Just like the 4.x and 3.2 versions they allow you to use the "Install" command with storage devices other than df0-df0 and cc0-cc1 and figure out the correct storage device driver for the respective device (e.g. it determines that df0 is associated with trackdisk.device unit 0 instead of assuming that df0 must correspond to trackdisk.device unit 0). Unlike the 4.x and 3.2 versions, however, they are less paranoid when it comes to check if the storage device should have a boot block installed on it. Also, the 4.x and 3.2 versions
really verify if the boot block found on such a storage device features a correct checksum (none of the other versions ever did that).
That's the (perhaps overly) long explanation
You should be unable to destroy your hard disk or USB stick partitions using the "Install" command, but you should not need to use the "Install" command on these either if you have already used HDToolbox (or a more capable and less quirky/brittle such partitioning tool) to set up a storage device. The "Install" command is really just for storage devices which the Amiga operating system considers special (such as df0-df9 and cc0-cc9). For all other storage devices there would be a hard disk controller such as for the IDE or SCSI hardware in the Amiga 4000T which upon system startup looks for Amiga RDB partitioning information on its connected devices.