some records do not get propagated from log to `microprot_db`

Around 0.1-0.2% of jobs finish successfully without any complaints in either output or logs, but values from per-gene log index file do not get propagated to the `microprot_db.index`.

Possible source of the problem is function `snakemake_helpers.append_db()`

examples:
- GRAMNEG_T1D_3301
- GRAMNEG_T1D_4292
- GRAMNEG_T1D_6724
- GRAMNEG_T1D_7144
- GRAMNEG_T1D_7471
all targets are in: `/projects/microprot/results/Broad_targets_gramneg_T1D`

Start by inspecting the `snakemake_helpers.append_db()` function and compare the per-gene log index files with `microprot_db.index` for examples such as `GRAMNEG_T1D_3301` under `/projects/microprot/results/Broad_targets_gramneg_T1D`. Trace why successfully completed jobs can omit records despite producing no errors. Done means the affected records are consistently propagated to `microprot_db.index`.

Written by the indexing model from the issue text.