[mscheltienne]

Raw.crop(..., reset_first_samp=True) filtered the annotations while first_samp still held the cropped offset and never shifted their onsets, so they ended up late by first_time + tmin. The onsets are now shifted by first_time and _cropped_samp is reset before set_annotations. _first_samps / _last_samps are left untouched since they index the files, which also fixes reading wrong data from non-preloaded files and the wrong first_samp on concatenated raws.

Reproduction

import matplotlib.pyplot as plt
import mne
import numpy as np

mne.viz.set_browser_backend("matplotlib")
info = mne.create_info(["EEG1", "EEG2", "EEG3"], sfreq=100.0, ch_types="eeg")
data = np.zeros((3, 500))  # 5 s of data
data[:, 200:300] = 1.0  # square pulse from 2.0 to 3.0 s
raw = mne.io.RawArray(data, info)
raw.set_annotations(mne.Annotations(onset=2.0, duration=1.0, description="pulse"))

cropped = raw.copy().crop(tmin=1.0, tmax=4.0, reset_first_samp=True)
print(cropped.first_samp, cropped.annotations.onset)  # main: 0 [2.]  fix: 0 [1.]

kwargs = dict(
    start=0,
    scalings=dict(eeg=1.0),
    time_format="float",
    show_scrollbars=False,
    show_scalebars=False,
    block=False,
)
raw.plot(duration=5, **kwargs)  # annotation covers the pulse at 2-3 s
cropped.plot(duration=3, **kwargs)  # pulse now at 1-2 s, is the annotation too?
plt.show(block=True)

AI disclosure: Claude (Opus 5.5) implemented the fix and the test and produced the figure; I reviewed the changes.