I came across a similar problem last year. The trouble was with the
merge function of osmosis. It takes the bounding box of the output file,
from the first input file, regardless of the bounding boxes of the other
input files. But the data from all the input files is in the merged
file. I contacted the maintainer of osmosis about this but received no
reply. It may be that it is the intended behaviour, rather than a bug.

I worked around this problem, but it is not at all convenient. You
create the output file in uncompressed .osm format. This can result in a
large file. Then you edit the file with a hexadecimal editor, because it
will be too large to edit with a text editor. The bounds are very near
to the start of the file. Use the hexadecimal editor to overwrite the
bounds with the correct values. This way, you only need to rewrite one
cluster, not the whole file. (For Mac, Hex Fiend from ridiculousfish.com
is a good hex editor, free and open-source.)

I have a vague recollection that it is also possible to get the splitter
to ignore the bounds in the input file.
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