Note: Specific regions were substituted by <gene>, <chrom> and <pos> to hide sensitive information. Real usage did not contain brackets.

After combining region of interest locations with bedtools to build a new reference FASTA:

bedtools getfasta -fi <genome>.fasta -bed <regions_of_interest>.bed -name+

And then doing variant calling with this new reference, we obtain a chromosome (VCF column #CHROM) name structure like so:
<gene>::<chrom>:<pos>

Upon using bcftools concat to merge VCF files:

bcftools concat -a <file>.snp.vcf.gz <indel>.indel.vcf.gz -O v -o <file>.merged.vcf

This structure throws an error:

Checking the headers and starting positions of 2 files
[E::_regions_init_string] Could not parse the region(s): <gene>::<chrom>:<pos>

However, as of VCFv4.3 and later this structure should be legal. See the official VCFv4.3 changelog:

7.1 Changes to VCFv4.3
(...)
The VCF specification previously disallowed colons (‘:’) in contig names to avoid confusion when parsing
breakends, but this was unnecessary. Even with contig names containing colons, the breakend mate position
notation can be unambiguously parsed because the “:pos” part is always present.

This was tested on bcftools=1.20, installed from source code, and previously bcftools=1.15.1, installed on conda.

I tried to confirm which HTSlib version was being compiled, but I couldn't figure it out. Does the current release of bcftools support VCFv4.3 and later?