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
309949357,MDU6SXNzdWUzMDk5NDkzNTc=,2029,Can't re-save netCDF after opening it and modifying it?,37649,closed,0,,,4,2018-03-30T01:16:11Z,2019-01-06T10:46:40Z,2018-03-31T22:30:50Z,NONE,,,,"#### Code Sample, copy-pastable

```python
import xarray as xr
import numpy as np
import pandas as pd

filename = 'foo.nc'

print('creating fresh file')
temp = 15 + 8 * np.random.randn(2, 2, 3)
precip = 10 * np.random.rand(2, 2, 3)
lon = [[-99.83, -99.32], [-99.79, -99.23]]
lat = [[42.25, 42.21], [42.63, 42.59]]
ds = xr.Dataset(
    {
        'temperature': (['x', 'y', 'time'], temp),
        'precipitation': (['x', 'y', 'time'], precip)
    },
    coords={
        'lon': (['x', 'y'], lon),
        'lat': (['x', 'y'], lat),
        'time': pd.date_range('2014-09-06', periods=3),
        'reference_time': pd.Timestamp('2014-09-05')
    })
ds.to_netcdf(filename)

del ds

ds = xr.open_dataset(filename, autoclose=True)
print('opened file')
print(ds['temperature'])
ds['temperature'][0, 0, 0] += 1000

ds.to_netcdf(filename) ### Crashes

# import os
# ds.to_netcdf(filename + '2')
# os.rename(filename + '2', filename)
```
#### Problem description

```
<snipped very long stacktrace, can produce if desired>
OSError: [Errno -51] NetCDF: Unknown file format: b'/path/to/foo.nc'
```
I encountered this problem when opening a netCDF file, modifying it, and trying to save it back. This is with `netCDF4==1.3.1` and `scipy==1.0.1`. (Potentially related: #2019?)

#### Expected Output

If instead of `to_netcdf` overwriting the just-opened file, I write to a new file and then `os.rename` (see the three commented lines above) the new file to the original location, all is well. `ncdump` reports that my change took.

#### Output of ``xr.show_versions()``

<details>
INSTALLED VERSIONS

commit: None
python: 3.6.4.final.0
python-bits: 64
OS: Darwin
OS-release: 17.4.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

xarray: 0.10.2
pandas: 0.22.0
numpy: 1.14.2
scipy: 1.0.1
netCDF4: 1.3.1
h5netcdf: None
h5py: None
Nio: None
zarr: None
bottleneck: None
cyordereddict: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
setuptools: 39.0.1
pip: 9.0.3
conda: None
pytest: None
IPython: 6.2.1
sphinx: None

</details>
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