i[f] you read it as a key value pair, then the values that get appended are lost

Not at all. The code line:

my ($k, $v) = split /=/, $_, 2;
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splits each data line into two parts: the part to the left of the first = character — which is assigned to $k — and the entire part to the right of the first = character — which is assigned to $v. So nothing is lost. In your example, the batch file would contain:

set VAL=<some path>:%VAL%
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and if VAL already contained, say, /bin, the result would be the assignment of VAL to $k and of <some path>:/bin to $v. See split:

If LIMIT is specified and positive, it represents the maximum number of fields into which the EXPR may be split; in other words, LIMIT is one greater than the maximum number of times EXPR may be split.

Hope that helps,