id,node_id,number,title,user,state,locked,assignee,milestone,comments,created_at,updated_at,closed_at,author_association,active_lock_reason,draft,pull_request,body,reactions,performed_via_github_app,state_reason,repo,type
1643408278,I_kwDOAMm_X85h9GuW,7691,`nan` values appearing when saving and loading from `netCDF` due to encoding,42553970,closed,0,,,11,2023-03-28T07:58:21Z,2024-03-15T16:31:06Z,2024-03-15T16:31:05Z,NONE,,,,"### What happened?

When writing to and reading my dataset from `netCDF` using `ds.to_netcdf()` and `xr.open_dataset(...)`, `xarray` creates `nan` values where previously number values (`float32`) where.

The issue seems related to the `encoding` used for the original dataset, which causes the data to be stored as `short`. During loading, the stored values then collide with `_FillValue` leading to the numbers being interpreted as `nan`.

### What did you expect to happen?

Values after saving & loading should be the same as before saving.

### Minimal Complete Verifiable Example

```Python
We had a back-and-forth on SO about this, I hope it's fine to just refer to it here:

https://stackoverflow.com/a/75806771/11318472
```


### MVCE confirmation

- [ ] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- [ ] Complete example — the example is self-contained, including all data and the text of any traceback.
- [ ] Verifiable example — the example copy & pastes into an IPython prompt or [Binder notebook](https://mybinder.org/v2/gh/pydata/xarray/main?urlpath=lab/tree/doc/examples/blank_template.ipynb), returning the result.
- [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

### Relevant log output

```Python
See the SO link above.
```


### Anything else we need to know?

I'm not sure whether this should be considered a bug or just a combination of conflicting features. My current workaround is resetting the `encoding` and letting `xarray` decide to store as `float` instead of `short` (cf. https://github.com/pydata/xarray/issues/7686).

### Environment

<details>

INSTALLED VERSIONS
------------------
commit: None
python: 3.11.0 | packaged by conda-forge | (main, Oct 25 2022, 06:24:40) [GCC 10.4.0]
python-bits: 64
OS: Linux
OS-release: 5.15.90.1-microsoft-standard-WSL2
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: C.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.8.1

xarray: 2022.11.0
pandas: 1.5.2
numpy: 1.23.5
scipy: 1.10.0
netCDF4: 1.6.2
pydap: None
h5netcdf: 1.1.0
h5py: 3.8.0
Nio: None
zarr: 2.13.6
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: 1.3.3
cfgrib: None
iris: None
bottleneck: 1.3.5
dask: 2022.02.1
distributed: 2022.2.1
matplotlib: 3.6.2
cartopy: None
seaborn: None
numbagg: None
fsspec: 2022.11.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 65.5.1
pip: 22.3.1
conda: None
pytest: 7.2.0
IPython: 8.11.0
sphinx: None

</details>
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